Hmm, maybe I misunderstand what you want to do - but that works fine for me (on windows) - (are you on a different OS)?

Otherwise, try installing Powertoys - that comes with FancyZones and gives you more control over how window snapping should work.

and different tool windows run when debugging so I have to reposition the pane boundary’s again whenever switching between run/design time.

Also isn't this a one-time-activity? Once you've put them in place, for me it remembers where it should be. Otherwise, I suppose in visual studio you can also manually save the layout (Window -> Save Window Layout) and then restore it again later (Window -> Apply Window Layout)