You can't even choose your party members in this full fledged mainline FF. If that's not a sign of padding, than I don't know what else is.
I half agree with most of what you said, but if there is something that's not a sign of padding, it's that, it's the opposite.
The reason you can't choose your character is because, unlike in the original, having a variable party composition necessitates a BUNCH more work when it comes to design, mechanics, and most of all, cutscenes. Each of which require extra motion capture, voice acting, and a ton of extra work.
That makes it completely infeasible to do for a character driven story heavy game like FFVII: Remake.
Ironically, the only places you can easily design with character swapping, is in areas that are just padding and therefore don't have character moments.
To me what is padding depends on the purpose of the scene, and whether or not it adds something to either the characters, or the story.
Chapter 4, to me, wasn't padding, because it expanded on Jessie as a character, and built on Clouds relationship with the Avalanche members. It also tied into the blasting agent sub-plot, which was all fine. The only part there that I consider to be padding, are the arena battles themselves, because those were clearly just a string of subsequent battles meant to increase runtime, instead of giving us an actual piece of gameplay where we sneak in and get the blasting agent.
While I consider chapter 6, chapter 17, and the train graveyard to be padded, I don't consider the chapters themselves to be padding, I think important parts happen in each and every one of those, and I think gameplay itself is part of the game, just because a part deals mostly with mechanics and actual gaming, doesn't make it padding. Gaming is the point of games.
But I can concede that some of them went on too long, or didn't do enough with their time to justify the padding, not enough character building, etc.
The one that to me really didn't earn it's inclusion though was the deepground bs, as well as many of the aerith sidequests and especially the chapter 14 sidequests.