I wouldn't call them major problems. There are workarounds for running things without much effort if you want, e.g. FHS or steam run or distro box. For Python, you can create a virtual env and use it like any other machine.

And if you do put in the effort to make a package, you'll never have problems figuring out how to install it in the future, and can share that gain with others.

Making packages for nix is way easier than making debs or rpms in my experience.