Greg,
I just bootstrapped git commit 87758334b887d5575e9c94a176a92f4cab4967c0
yesterday on RHEL 8.5. No issues at all (that weren't caused by me making
mistakes). With respect to GUI applications, I have i3, i3lock, dmenu,
mpv, zathura, and fontforge working without any issue, fonts are correct,
audio worked without any kind of additional configuration, etc.
Sijmen, the lack of shortcuts doesn't affect me using i3, but the shortcuts are
definitely being created correctly in /usr/pkg/share/{applications,xsessions}.
This is and has always, afaik, been expected behaviour. The base system
doesn't know to look for shortcuts from pkgsrc unless you tell it to do so.
If you install and use a WM from pkgsrc, I would think it would pick them
up correctly (but possibly not the ones installed in the base system).