I've been playing around with Syriac layout with PBB the last couple of days. My observations should also be applicable to Arabic, Aramaic, Hebrew, and any of the other Right-To-Left languages.
It is possible to get proper layout with RTL languages. Here is an example showing my source document and the formatted PBB:


However, inserting milestones causes layout problems. Specifically, where the milestone appears in the text it disrupts the proper RTL flow of the text. The following is a PBB of the UBS Peshitta NT text. It has milestones in the format
[[@Bible:Matt x:x]] at the beginning of each verse (before the verse number). If I don't add the milestones the text has proper layout. If I add the milestone they work as milestones but text is displaced. Following is the source document and the PBB document. I will circle the text of Matt 1:1 in both.


As you can see, the milestones cause the text to misplace. On the second line the remainder of verse one is displaced to the left of the line, after the first part of verse 2 text. The layout is proper if the ONLY change I make is to not have the milestone tags in the source.