when I select two compound paths and subtract, I get a fully selected group.
If I create an action consisting of just the pathfinder operation and run it from the actions panel, the result is identical.
If I call this action from extendscript, the group sometimes is only partially selected. - and the following steps produce unexpected results :(
It turns out that adding an extra object.selected = true can help.
I observed this in 2022 edition, I have the impression that this did not happen in 2020 edition