But the permission you're perceiving with Rule Zero does nothing to address knock on effects. It doesn't seem to address the concern you're expressing here.
True, not directly, but what it does do is explicitly communicate to me that the structure of the game is expressly designed to take modification in stride. 5e specifically calls out the three changes that will unbalance the combat chassis. The combination of those two (not to mention the extensive optional rules section) gives me confidence that changes made, outside of those three exemptions, are less likely to have the negative consequences I'd rather avoid.
I contrast this with Blades in the Dark, which talks instead about the game is designed to "fail gracefully" if sections of the rules are forgotten or ignored. Which, is still reassuring, but in a very different context. It expressly says "
The game is better when you use all the details, but the whole thing doesn’t come crashing down if you don’t." This sort of language actively works to suppress any desire I might have otherwise had to modify the game to fit my purposes. Which I think is the right call for Blades! It's got a lot of interlocking systems, and if I mess with, say, Stress, than that is going to potentially affect flashbacks, vices, trauma, devil's bargains, rituals, etc. When I play a game as specific as that, I want to try and follow the designers' intentions, so that I have the envisioned experience and can examine it on its proper merits. And that's what I'm looking for out of Blades, I've seen very convincing arguments about how the game is so very pointedly crafted to create the pressure-cooker environment that forces characters to act both appropriately and in exciting ways. In addition, I read posts on here that talk about GMs that run PBtAs and the like in "degenerate" form, and how they are fundamentally not actually playing the game they say they are because of misapplied principles. I'm quite concerned about ending up there just by failing to fully embody the agendas, which I already struggle to keep as forefront in mind as I'd like. Intentionally changing the rules text feels even more likely to push play into that state.
To be fair, I do know the rulebook has a section called Changing the Game, and there are extensive and varied options there. That does help to empower me, but only to the degree that I would probably generally limit myself to the options that are called out there, having been vetted by the creators.
And, to this:
I think the instinct you expressed above about unclear situations would guide you best here, as well.
That's very fair, and I probably worry more than is strictly necessary. But, I worry more than is strictly necessary about roughly 83% of the things in my life, so I can't say it's a surprising call out, nor do I think it's an issue I'm likely to leave behind me anytime soon.