I accept that I'm in the minority on these things, but I value simplicity really highly, and I mean "simple" as a very specific concept that's different from "easy". It can be harder to resolve library dependencies on a system where everything is installed using the native package manager and common file systems, but nothing is as "simple" as ELF binaries linking to .so files. Nested directories branching off of / is "simpler" than containers.
Do I have any practical reason for preferring things this way? Not really. There are some ancillary benefits that come from the fact that I'm old and I already know how to do more or less anything I need to do on a Unix system, and if you tell me I need to use flatseal or whatever, I'd rather just use users and groups and tools that have been fine for me for 25 years. But that's not really why I like things this way. I have no issue with embracing change when it otherwise appeals to me --I happily try new languages and tools and technology stacks all the time. What it really is is that it appeals to the part of my brain that just wants to have a nice orderly universe that fits into a smaller set of conceptual boxes. I have a conceptual box for how my OS runs software, and filling that box with lots of other smaller little different boxes for flatpack and pyenv and whatever feels worse to me.
If they solved practical problems that I needed help solving, that would be fine. I have no problem adopting something new that improves my life and then complaining about all the ways I wish they'd done it better. But this just isn't really a problem I have ever really needed much help with. I've used many Unix systems and Linux distributions as my full-time daily use systems since about 1998, and I've never really had to spend much effort on dependency resolution. I've never been hacked because I gave some software permissions it wouldn't have had in a sandbox. I don't think those problems aren't real, and if solving them for other people is a positive, then go nuts. I'm just saying that for me, they're not upsides I really want to pay anything for, and the complexity costs are higher than whatever that threshold is for me.