It occurred to me both programs still use the same library as well as the same name for the whole filetree (including the executable bits) which is why it is hard for them to coexist on the same system.
So I installed DT from the Manjaro repos in the usual fashion. It uses /usr as base installation (so /usr/share, /usr/bin etc.) and ~/.config/darktable/
I compiled and installed R&Darktable into /opt (so /opt/bin, /opt/lib, /opt/share etc.) and I’m starting it with a Desktop file which has the commandline
/opt/R-Darktable/bin/darktable --configdir /home/mike/.config/r-darktable %U
And that seems to do the trick. Both installs have their own config and neither complains about the library version. Both can be updated individually as well.