How the hell the father could have chakra? We saw Hago as a spirit... I f something happened in his body he would know. He watched his children fight too. And if Hago's had survived then BZ wouldn't go all the trouble to get the Rinnegan from the reincarnations...
Kaguya was the first on earth to have chakra after eating the fruit.
That tree was born out of the blood of many people or something like that. Who's to say it might've not happened in other planets as well. Ootsutsuki's have the Byakugan which are able to locate chakra (apparently Kaguya's clan descended to earth for the sole purpose of eating the fruit. As a result, she stopped all wars and stayed on earth for whatever reason). Though she was still placing people under IT during her reign. Kinda seems like she was still looking for more power and an army even back then so this new guy could've already been lurking around. If that's the case then it wouldn't be Hago's and Hamu's ocular powers but I'd also take it as if they might've inherited the powers from him and the chakra from Kaguya.
They're not human remember? The fact that Kaguya was building an army to fight someone shows that this individual must've had some strength. Going to earth to use it as a nursery to build an army to fight some weak guy who she could've killed at any time doesn't sound right.
As for it being Hagoromo and Hamura's eyes, you're right. I said it would be interesting but practically impossible in my opinion for two reasons.
1. I'd assume that they'd know about it. They're ghosts and all but they've been keeping tabs on the living. Though there are some things that went unnoticed. Hagoromo didn't even realize there was a black blob trying to bring his mother back.
2. If this guy got their eyes after their deaths, then why was Kaguya even trying to build an army in the past? Why did she even need more power to fight this threat if the main source of his power (At least I assume it is) was acquired after she was sealed away. Not to mention, transplanted eyes aren't better compared to the original wielder.
Regardless I doubt they're Madara's. When Kaguya came back, she tried to do the same thing (BZ gave hints along the way). Madara wasn't dead yet and the Rinnegan was still with him. Unless you're implying he was already extremely powerful and simply decided to get more power.
And sorry you had to read all that if you actually read it.