When Z shell is run as a login shell, /etc/zshrc unconditionally overwrites the PROMPT after the scripts in /etc/profile.d have been sourced. This prevents Toolbox from prefixing a hexagon indicator to the prompt like it does for Bash. It might be nicer if /etc/zshrc overwrote the PROMPT only it's set to Z shell's built-in default of '%m%# ', just like it's done in /etc/bashrc.
Pull request: https://src.fedoraproject.org/rpms/zsh/pull-request/5
Merged, thanks! Fedora commit: https://src.fedoraproject.org/rpms/zsh/c/20551698
Wow, thanks, Kamil!