The number of the URL follows the site content language, which is English here on Translatewiki. When LQT is enabled on a Persian wiki, it will be in Persian numbers.
It is not possible to have Persian numbers in a URL on a non-Persian wiki.
Yes, I installed that on a local Persian wiki (not here!) and lqt had bug on Persians numbers. I wanted to report the bug from here (not bugzilla :D)
Sorry, I didn't know that now you are working on Persian language on non-Persian wikis, Is this done by an extension? It is great (and far more better than commonswiki's localization)
I am fixing a lot of bugs of RTL languages. More improvements coming soon. I aim the site here to be nearly perfect :) And it will be in the software by default soon, and it will reach Commons and other wikis by the end of this year or the start of next year. So if you have feedback or bugs, please say! (Btw, I will look at the issue you said, when I have time.)
First thing that I can see somewhere in mediawiki UI (same #p-views > ul and #p-personal > ul) have lang="fa" dir="rtl" but #mw-panel have not, also #mw-clearyourcache (on this page) have not lang="fa". It is a minor problem but can you see what happened?
I fixed the reply count in mwr:91528.
As for the lang="fa" dir="rtl" attributes, I can add it, but is it needed? Are there problems with it?