I don't think the two can be played together since windower isn't launching the steam overlay.
Yeah that's what I'm guessing. There's so many external launching initiations that it doesn't surprise me that the steam UI drops off at some point since it only allows one designated target from launch.
I think if you add windower to steam as a nonsteam app then run it, i think you can get the steam overlay in windower.
Tried it. Steam recognizes me running windower up until the point where it jumps into POL.