The problem here is that:
1. For starters, when it comes to Pain (in that early panel you posted), you can actually still see the concentric circles of the rinnegan. You just see fewer of them, but it should be noted that Pain was silhouetted and his head was turned at a certain angle. Having said this, it is possible that there was no design change there, and that it was just crudely drawn at the time.
It is also possible that Kishi didn't really have a plan or concept of the rinnegan that early in the series (which by the way is unlike the mangekyou sharingan which Kishi had long since established in multiple characters by the time he first depicted Indra in that mural-esque fashion).
What's more, even if there was a design change in the rinnegan, both the original design and the change were both depicted in the manga itself (whereas Indra with Sasuke's mangekyou was not depicted in the manga). That is one of the reasons why the so called "design change" in the rinnegan is more accepted than that of Indra's mangekyou sharingan.
2. Additionally, when it comes to Indra and the mangekyou:
In the manga, we haven't had a single instance of two Uchihas having the same mangekyou pattern (save for the Shins, but they are literal clones of each other).
Plus, Indra having Sasuke's mangekyou is a huge slap in the face to Madara and all other Indra transmigrants.
We know that it is not a matter of the fact that Kishi or SP couldn't think of any unique mangekyou designs (after all, they thought up some filler MS designs for some filler Uchihas and even one for Fugaku). They were just trying way too hard to hammer home the emphasis on the fact that Sasuke is Indra's transmigrant (and that wasn't necessary).
In the end, many fans (myself included) are not willing to accept that Indra had the exact same MS as Sasuke (essentially saying "screw you" to Madara and all other transmigrants). That is probably the other reason why many fans say that the Otsutsuki episodes were filler.
Anyway, I agree with you and Bad Touch Yakushi that the concept of filler and canon is toxic at large. You should just enjoy it regardless. However, when it comes to Indra specifically, I am still on the side that says that there is no way he had Sasuke's mangekyou.