is there something in your .profile, bashrc or zshrc BEFORE you install fleek that needs to be preserved after? can you look at the backup files it makes?
I looked into it. fleek applyfleek apply does indeed replace .bash_profile and .bashrc files with their own - that is, with symbolic links pointing to root/root 'real' files stored within nix's home-manager.
Can you open an issue on fleeks repo with the parts that are missing? Maybe we can figure out a way to either set them somewhere else or do a special case for bazzite