I’ve also worked with Bible Modules in a RTL (Arabic-like) language.
The problem you’re showing \ref GEN 1:1-31 looks much like what I also see. I think this isn’t completely a problem with PT, but is simply an artifact of switching back and forth between RTL and LTR languages. In particular, the Unicode Bidi algorithm does things with : and - which don’t make sense to me (one of the two reverses the visual order in RTL languages, the other doesn’t), but people smarter than me maintain that it really does work–or at least fit the greatest possible number of language expectations.
One thing that I’ve eventually learned to do is simply be able to reinterpret the visual order back into what the actual order is. At times, if that doesn’t work, I delete the reference and retype it in the order I know it should be, ignoring what’s actually displaying on the screen. The Bible Module referencing system needs the underlying unicode characters in the correct order and doesn’t care about what it looks like visually.
One other thing I do is use Notepad++, which has easy key commands (Ctrl-Alt-r and Ctrl-Alt-l) to quickly switch back and forth between RTL and LTR. This allows me to work in LTR order for typing references and things like that, then switch to RTL order for typing the local language, etc.