In an RTL Paratext project, I have not found any combination of Scripture Reference Settings and verse text and module specification that all work together happily.
Scripture references must have an RTL mark (U+200f) before elements such as the chapter-verse separator (:), the verse range separator (-), and the chapter range separator (U+2014). The verse text has these RTL marks correctly.
The only way I can get references to be generated correctly in a module, such as from $(PRO 3:13-26), is to include the RTL marks in the definitions of the various separators in the Scripture Reference Settings.
However, if such marks are included there, then the reference checks for the verse text gives errors like this:
MAT 1:0 Invalid chapter/verse separator: ~~||:||~~
I can only get reference checks to pass by removing the RTL marks from the Scripture Reference Settings, but that breaks the module output, which then no longer includes RTL marks.
One highly clunky workaround is to remove the RTL marks from the Scripture Reference settings, ignore the appearance in the modules, and add rules in every output to insert the RTL marks, such as in Scripture App Builder, in Publishing Assistant, etc. But there must be a way for Paratext to get this right?