Distro agnostic packages like flatpaks and appimages have become extremely popular over the past few years, yet they seem to get a lot of dirt thrown on them because they are super bloated (since they bring all their dependencies with them).
NixPkgs are also distro agnostic, but they are about as light as regular system packages (.deb/.rpm/.PKG) all the while having an impressive 80 000 packages in their repos.
I don’t get why more people aren’t using them, sure they do need some tweaking but so do flatpaks, my main theory is that there are no graphical installer for them and the CLI installer is lacking (no progress bar, no ETA, strange syntax) I’m also scared that there is a downside to them I dont know about.
That is not at all true.
There is one explicit case where “system libraries” are used by Nix programs and that is graphics drivers. This is not done outside of NixOS as it does not trivially work there; it’s still an open problem. We can discuss about the reasons for this impurity’s existance and its intricacies but all that is important here that this impurity is the sole exception, not the norm.
Apart from that, Nix will never under any circumstances load (much less modify) libraries of any kind from any global path; system-controlled, user-controlled or otherwise. That’d be contrary to the fundamental principles of Nix.
It will always use “specific library versions separate from your system libraries” aka. the explicitly and exhaustively precisely declared dependencies in the Nix store. That’s the whole point of it.
I’d recommend you read up on Nix again and revise your opinion once you understand what it actually does because it’s clear that whatever source you had for information on Nix was entirely wrong.