I don’t know how BSD works, but linux has $XDG_ configs in homedir of user for most configuration files.

You could sidestep any conflicts by just changing your linux-systems $XDG_ -environmental variables to something like ~/.local.linux, ~/.config.linux and so on.

Ultimately almost any path under $HOME can ba changed with corresponding environmental variable in linux - so you can split directories if necessary.

Not really, no. The only hypothetical issue is configs between your programs clashing due to version differences. IME, though, that’s a rare problem except with maybe Firefox, which can be a stickler for version numbers.