Howdy Taelan and welcome to the forums!

with keyclone, you can currently set 1 window to always be on top, thereby giving you that look. but if you pip swap it, you would want the 'topness' to swap as well.. and it's not associated with the region, but with the window.

i put it on the list... to move the 'always on top' from the command to the region. this should work as you expect