There seems to be an issue with the Lam-Alif ligature with Hamza on top of Alif in InDesign: the Hamza appears above the Lam in stead of above the Alif:
This does not happen consistently, and I cannot isolate what causes this. This happens in Indesign (windows) 18.5 and 19.4, and gets exported like this to PDF.
I’m glad you have a work around. Our code specifically positions the diacritics so we haven’t really thought about how an application might change the position. I’m not sure we want to go there!
Anyway, I also wanted to comment that our latest fonts have different weights, so instead of italicizing the Arabic text (which is certainly unusual) you may just want to choose a different weight to make it look different.