Exactly. I love Zelda games because of the progression in each dungeon (also why I didn't like BotW much). The dungeons themselves are rarely challenging (some bosses can be though), and the puzzles are mostly interesting because you use tools you've collected along the way, sometimes in ways you didn't think of at first. You may do something a certain way in dungeon A, and then when you get a new tool, you see something similar but solve it differently (i.e. the old way is blocked) using the new tool. It all builds on each other.

Standalone dungeons miss that context.

That said, maybe it makes sense in TotK because it likely has BotW-like shrines that aren't tied to progression elsewhere. Idk, I didn't play it because I was disappointed w/ BotW.

I suspect it's more about the difficulty of generalizing a bug-free experience. Nintendo likely has internal tools which do this in a relatively reasonable and user friendly way, with the major caveat that it relies on a QA stage for production viability. The complexity is just too high to not have that safety net, so turning users loose on it would just make the experience too unstable to be viable.