The first part about the Jogan is absolute horseshit. If it were the case that the mixture of the two chakra's produced the Jogan then Kaguya would've had it. The reason he has it is because he didn't have enough handouts. And there's been 0 foreshadow of it being connected to Hamura and Hogaromo's chakra.
1. The gene itself didn't give Madara the eye. He had an active eye that achieved it's final stage. It didn't go beyond that or become something new it was the final progression. So that points out of the window.
2. It's called Sharingan in the manga but anyway eating the fruit is an assumption as she is the Jyuubi. She absorbed it somehow and got the "rinne sharingan" something the Jyubi already possessed.
3. Was a blatantly badly written ass pull, but even then Obito was one of the few Rokudo's to exist. Boruto isn't and never was.
The other ass pulls are confirmed.
No he doesn't he confirmed in the manga he didn't train for any of the 3 elements. Go back to his boast in the Hokage's office. And according to the databook entry he even had purple lighting alongside other elements at the time. Naruto only praised Boruto's rasengan and even then Boruto didn't confirm he was training. Even then in the second bout Boruto shrugged off Naruto's praise of so called training with "you could say that."
Handout seal, yes it does. The whole plot is based around the seal and it wasn't foreshadowed. And it was given for the heck of it. Yes plot devices require foreshadowing for MCs anyway otherwise anybody could pull any shit out of their ass.
Healing ability is connected and another handout. It's pretty obvious there's plot relevance but it's still another ass pulled handout.
Unlimited chakra - yes he does. He doesn't run out. The reason taju SCJ is a forbidden jutsu and not everybody under the sun uses it is because it burns out your chakra. If the law of division is applied then when then Boruto would be down to between 20 and 25% chakra. Then the next division would reduce it even further. However, the walking ass pull factory has an unlimited supply until the job is done.
Adding nature is the hardest thing, Minato, Kakashi and Naruto all failed. Naruto trained for that skill using 000's of clones until he developed it. Borat just pulled it out of his ass without even training it.
1. About Kaguya: You say that Kaguya would have had jougan if it was a mix of Hagoromo's and Hamura's chakaras, but that isn't necessarily true. Hagoromo's chakara may have been Indra + Asura, but that doesn't mean that every parent's chakara is child 1 + child 2. Kaguya clearly had stuff in her bloodline that neither of her kids seemed to directly inherit despite some of this stuff appearing in later descendants. The ash bone kekkei mora is a prime example of what I am talking about. Neither Hagoromo nor Hamura inherited this nor the diluted descendant version which turned out to be the KKG of the Kaguya clan (Kimmimaro's clan).
Also, Kaguya's children inherited things that Kaguya herself did not possess such as the tenseigan. This shows that there were other factors in Kaguya's genes and bloodline other than just Hagoromo + Hamura, and that Kaguya's descendants can inherit things that she herself did not possess.
2. About Kaguya awakening the rinnesharingan: You say that Kaguya got it from being the juubi and you said that the juubi "already possessed it". However, you don't seem to realize that Kaguya predates the juubi. She ate the chakara fruit and awakened her power (including the rinnesharingan) long before becoming the juubi. She became the juubi years later when she merged with the shinju in order to defeat her sons and take their chakara. Prior to the fight with her sons, Kaguya had been placing the populace under the infinite tsukuyomi (which requires the rinnesharingan) in order to turn them into white zetsus for her army that she was going to use to fight Momoshiki and the other Otsutsuki clan members. Hagoromo and Hamura opposed Kaguya's actions, and that led to Kaguya merging with the shinju (thus becoming the juubi) in order to fight her sons.
3. About the nomenclature of the rinnesharingan: I know that Hagoromo called it a sharingan in the manga. However Sasuke called it a rinnegan. When the infinite tsukuyomi was casted, the victims had the rinnegan in their eyes and Sasuke's rinnegan is what made him immune to the infinite tsukuyomi. Undoing the infinite tsukuyomi requires the chakara of all 9 bijuus and the rinnegan. In short, it displays a lot of sharingan properties and a lot of rinnegan properties and it has been referred to as both. That is why I am not comfortable just calling it a sharingan. It is clearly vastly different from the eye of Indra and the Uchiha clan, and as such, it warrants a distinction in its nomenclature. That is why I use rinnesharingan.
4. About Madara: Yes Madara had an active eye, but that is happenstance. Who is to say that Madara wouldn't have awakened the rinnegan had he merged Indra's/Asura's chakaras even without ever awakening the sharingan? Who is to say that kid Madara (pre sharingan) couldn't have taken kid Hashirama's DNA, waited for several decades (without ever fighting another battle or awakening the sharingan) and then awakened the rinnegan when he was about to die like he did canonically? Hagoromo never stated that an active sharingan was necessary to awaken the rinnegan. In fact, he never said that sharingan was necessary at all. We just assume that it is because neither Naruto nor Asura awakened the rinnegan even with Hagoromo's chakara. As for Kabuto stating rinnegan to be a natural evolution of the sharingan (as well as old Madara), they were close. However, Kishi (through Hagoromo) retconned the Uchiha + Senju = rinnegan thing and replaced it with Indra + Asura = Hagoromo, thus leading to rinnegan. He basically made it so that only a transmigrant can awaken it. In other words, something such as Itachi taking Tobirama's DNA would not produce the rinnegan.
In short, what I'm saying is that rinnegan is not simply a natural evolution of the sharingan (a fact that is further proved by the fact that you can awaken rinnegan without having a sharingan or at least without awakening it as evidenced by Momoshiki who as of now is not known to have ever possessed a sharingan). Rinnegan can be awakened on its own via the right chakara or chakara fruit. As for where the whole dojutsu gene thing comes in, honestly I only put that in there because as I said before, Naruto and Asura didn't get rinnegan despite receiving Hagoromo's chakara. Nevertheless, Momoshiki shows that skipping the sharingan stage (if any part of sharingan is necessary at all) is entirely possible with the right chakara. As far as the manga goes, Hagoromo shows this as well (the anime filler is a different story).
Having said this, who is to say that Boruto couldn't skip the byakugan stage and just awaken the jougan based on the chakaras that he may have been influenced by from his parents?
5. About Obito giving Kakashi sharingan through chakara: You can call it an asspull or you can call it bad writing, but that doesn't make it any less canon. Therefore, asspull or not, it still stands as proof that chakaras can lead to dojutsu.
6. One thing that I always notice that you don't address: You say that Boruto has the jougan because he needed more asspulls and handouts, but that is an out of universe reason as to why he has it. Whether you like it or not, we are eventually going to get an in universe reason (something that actually has to do with chakara, genes, transmigration, bijuus, and other in universe elements). The jougan is too important of a plot point for it not to be explained. Having said that, if it's not due to Otsutsuki chakara or bijuu chakara or byakugan mutations or anything like that, then what in the world would his in universe reason for having the jougan be?
I know that you passionately hate Boruto, but don't let your hatred delude you into thinking that the concept of "asspulls" and "bad writing" actually exists in universe to the characters themselves.