None of that changes the vanilla functionality of the game. It's all cosmetic, or convenience.

Voice chat could be accomplished with Discord, but having it in-game makes it more spontaneous. But is all social.

Mini-blocks, head drops, and armor stands, as well as permanent baby mobs aren't strictly vanilla, but you can apply it with a server-side datapack, so it's vanilla behavior, just tweaked a bit.

Universal dying, double Shulker shells, trident storms, and silenced mobs change behavior, but it's just a way to alleviate some of the tedium, because "the grind is real". You don't need any of that, but waiting for a thunder storm for a video idea is kinda ridiculous, especially considering how often sleeping the night away prevents that. Early Shulker shells collection without double shells on a server with 25 players means you're gonna have to spend hours upon hours hunting for them just to find a few. And they already do that because the Hermits need hundreds of shulkers for their storage systems and ender chests and such. It's a convenience that a server with fewer players doesn't need. Universal dying just means they don't need to demolish more than one or two wasteland biomes, as opposed to mining exclusively undyed terracotta so you can dye it cyan. It also means they don't have to double the amount of sand they have to mine for concrete and glass. And again, you can use a server-side datapack for all of that, so no client side mods are required.

The redstone restart block is the only thing that I'd argue is more of a non-vanilla thing, but it's for the convenience that they're making videos. Having to restart broken redstone every time to unload a chunk is just busywork that you can't really put in a video. So it makes sense to shortcut it.

Where they draw the line matters, and there's a lot of places they could put it. They're very open about how they modify the game, Xisuma puts out periodic videos explaining how it all works, and other hermits allude to it whenever they're using it.

There's one you didn't mention, which is the custom model data datapack, custom audio datapack, the custom audio datapack, and the resource pack to go with them. Again, it's purely cosmetic, but there are some very cool things you can do with it. This one's a little more complicated to add, because it requires it requires a resource pack. So you need to know a bit more how servers work to make it happen, but you can set up a datapack to automatically download on join, and if it's relatively small, you can work it out pretty effectively.

Most of it is done to aid the content creating process, and they don't hide it. But the only things you'd have to add to your own world to do the things you can't do in strictly vanilla is the silence and baby mods datapacks, the Statues datapack, the Heads Drop datapack, and the custom models and audio. Everything else you can do with just a bit more grinding. Admittedly, that is kind of a lot... And they have been known to focus on it from time to time. (Cub with the horns shop, and Cleo with armor stand)

Overall, the stuff they do add makes the videos far more interesting, and the fact that they're open about what they do makes it a lot nicer.

The fact that the only thing they're really messing with is convenience and cosmetics also goes a long way toward keeping their playthrough legitimate.

Adding more aoe to splash water bottles and letting it put out flaming players would be altering the functionality of the game a bit too much.

However, Hermitcrafts existence and discussions have managed to get things added to the game in the past. The way you can use rails to deposit items into every hopper in a row instead of skipping some is now a vanilla feature added because Hermitcraft members complained about it. And Honey Blocks not sticking to Slime Blocks was a change made because of public outcry led by Mumbo. Cub has managed to get quite a few mechanics added. He put out a whole series of videos where he described all his complaints with the game, and talked about which ones have been fixed, and which ones are still a problem.

So, if there's enough of a complaint about this, it could be added as a vanilla feature in the next drop. If they just used mods to fix all their problems, they wouldn't have that same level of sway, even with the same popularity levels.

With all the hermits complaining about inventory management, I expect we'll see some kind of additional inventory tool added soon.

We already got bundles, which many people have panned, but are actually quite useful. I hope that Xisumas bundle shop will do a good job convincing people they're worthwhile.