There are potentially cleaner approaches, but they require immensely more manpower than I could seriously consider mustering. There are options such as writing and upstreaming new system calls to implement some sort of union-filesystem/chroot() mix, which, based on past attempts to upstream a union filesystem into the kernel, won't happen. Other approach is to altering/packaging every single package I am interested in - including proprietary software - so that they play nicely together. Nix/NixOS is making an admirable attempt here, but they don't have the manpower to package enough things. For now, Nix is, sadly, academic.
Personally, I find that while it isn't the simplest system from a high-level design point of view, Bedrock Linux's approach is by far the most practical solution to the problem I aimed to remedy. And it works, and I'm running it now. It is certainly not for everyone or for every use case. I made it for my own uses, which it serves admirably. Enough people seemed interested that I made it available publicly. You're welcome to continue using whatever software stack you prefer - I don't intend to snag everyone. Or even very many people. I'm happy to be the only one using it. However, I do aim to share if there are others out there interested in it.