How to deal with alignment zones tha overlap in one master but not another

I have a typeface where in one end of the weight spectrum the alignment zones for the ascender and the cap height is the same but at the bolder end they’re separate, so half the family has valid alignment zones (not overlapping), the other half does not. What’s the best way to deal with this export?

I don’t know. It should be OK for the master where the zones are exactly the same. For the intermediate instance you have a technical problem (zones can’t overlap) and a geometrics/hinting problem. There is no way in CFF to get a proper result. That would only work in Truetype or CFF2 (the later is not supported in Glyphs, yet).

I got the same issue in one project and was wondering the same. Would it be possible to then favour one of the overlapping zones, so that the other one gets ignored?
I had the feeling that this case might not be to rare actually, as often the xheight should increase towards heavy weights, causing the ascenders to also change height non-linearly compared to th CapHeight.
But maybe those are rare cases actually.