Could you take a look at this solution Direnv, project environment and zsh - #12 by aameen and let me know if that resolves your issue?
I believe this might be similar.
If you explicitly set . <( flox activate -e '.#default'; ); it might do the trick. There’s some additional direnv for “project environments” snippets in this thread as well: Is it possible to change the name of a project environment after having created it? - #8 by aameen