Room

Indicators are never drawn over a window: apps draw their own title bars and toolbars, and nothing could sit on them safely. Instead Yabar asks yabai to leave room beside each stack, on spaces that hold stacks only:

• Padding on the side where a stack meets the screen.
• A wider gap where a stack has windows on every side.

yabai's padding is per side of a space, but its gap is one number for every split, so a stack whose chosen side faces another window turns to one that faces the screen: the opposite side first, then the two across. Only a stack boxed in on every side widens the gap.

The room is just enough for the indicators (icons 30 points, tabs 28, pills 11) and never less than your .yabairc's. Room grows the moment a stack needs it, and shrinks only once a smaller room has been asked for a quarter of a second, so a stack that comes apart for a moment while a window moves doesn't move every other window with it. A space whose room still keeps changing, four times in two seconds, keeps the larger room until its stacks change, and Yabar logs it (log show --predicate 'subsystem == "io.github.mpdreamz.yabar"').

Your .yabairc values come back when the last stack on a space goes, when indicators are off, and when Yabar quits, including a kill or a logout. After a crash, the next launch puts them back.