After quite a lot of fiddling, I’ve found something weird here.
This font doesn’t contain Latin, only Lao. So I had set the body height alignment zone like this:
As you see, it’s a custom name with a script filter.
This was giving incorrect results. Here’s a screenshot from Acrobat Reader at 10pt, where you see the letters with overshoot are a bit higher than the others, although the zones are definitely set correctly:
After researching was told, that zones with filters are not yet exported.
I found out, that those kind of zones are only supported in fonts with CFF2 tables
Glyphs just has this feature implemented already
Edit: read the whole thread and don’t answer after just reading the initial post.