I think the OGS behavior for “dead” stones in a seki is reasonable and I addressed that situation here: Auto-score improvements - #31 by hexahedron
M19 area, T19 - these are also eyes in seki and are not points in territory. As a deliberate choice, M19 and N19 are still counted as points for captures because they are marked as dead even though the territory underneath the stones is not (and should never be) counted. This is a slight departure from the Japanese rules that mandate that you physically capture such stones during play before ending the game. Given the realities of server play and interfaces it’s a deliberate choice from the scorer:
Behaving more strictly could require careful corresponding UI work, since if stones that users explicitly mark to be dead are sometimes not counted as points, it may be confusing for users, and it may not be easy to see or know when they are and are not.
(this was written from the perspective of the territory scorer code that is being handed a list of stones being marked dead by users. If the marks are AI-supplied, then it’s not an explicit choice of the users so this is less of an argument. But the users could still click to mark them and then we’d be back in this situation. Plus also it would be weird and result in weird complications if the scorer code was in the business of disputing the life and death markings it’s being given or choosing to confusingly disregard them)
This choice is also more “AI-resistant” in that AI ownership markings will likely always mark such stones as dead (because future play will trivially be able to kill them), and so we should just count them as points rather than confusing users with a magically tricky exception that in this one special case, marked-dead stones somehow don’t count as points.
Obviously, in this particular case black should capture them and force white to throw in once more, gaining an additional point, but it’s not the scorer’s job to determine that, so we deliberately score only 2 points here for the marked stones, not 3.