Follow-up Comment #4, bug #20295 (project mypaint):

Andrew: You shouldn't have to move any layers. There are already >1 areas of
paint which are invisible before the merge (because it's being applied in
Lighten mode and is not lighter than the BG), and which show up after the
merge. If it really does look the same before and after, that's a .. anti-bug?
(seeing as this is a bug report for how it DOESN'T look the same before and
after)

Martin: IMO the appropriate way to handle transparency control is to provide
some kind of masking, where the alpha channel of one layer masks the layers
atop it. I think it's not a big deal that the merged paint could be solid-er
as long as a way to do that is on it's.. way, especially considering that some
effort is made to avoid solidifying. In any case I absolutely agree that it's
the most predictable + reliable choice, and transparency is not a big deal.

GIMP-2.8 has the same behaviour as 2.6. Not sure about 2.9 (development
version), as GEGL introduced some changes in the way compositing is put
together.

Out of curiosity, what would the code do in this case I attached? (where the
best solution seems to be to decrease alpha to 0 for areas of no visible
effect)

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