MyPaint treats omitted isolation values as "auto", and unknown (my custom "test:something") as "isolate". I guess I should never omit this attribute.
On the other hand, Krita treats omitted as normal, but unknown as "auto", i.e. enables its Passthrough checkbox. Which seems to match what I suggested as isolation="pass-through" (i.e. apply opacity, but leak all blending operations including masks), which sort of works if that was intended by the user. But we still need working isolation="isolate-alpha" to keep transparency mask effects inside.
Also I found a bug in Krita (v4.4.3), I think: if a passthrough folder has partial opacity and visible (enabled) transparency mask layer with 100% opacity directly nested inside (not some levels deeper), then folder opacity seems to apply twice, maybe first to mask and then again to folder. Partial opacity of the mask layer and 100% opacity of the folder only applies once as expected.