Per title, with the same file the 3 autohinter (or whatever deals with alignment zones) behaves very differently than 2’s. See screenshots:
g2 
g3
I have custom metrics on 3, not sure if relevant.
Can you send me the .glyphs file?
And where do you test this?
I sent you the file. The screenshots are from Indesign on Big Sur 11.1
There are two problems.
First, your “Actual A/Descender” will not be use for the autohinting as only the default ones are used (this is a limit of the font format). You should set the vertical metrics in the masters to match the design. If you need different values for adjusting the line spacing, add specific custom parameters (typoAscender …).
And I just recently changed the auto hinting code and made a small mistake.
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