I see what you mean. I truthfully don't usually swap and instead leave ctrl-left as is and just re-assign capslock elsewhere (e.g. win-right, or another chord) as the habit of which key to hit for ctrl is hard for me to break. AltGr at least still works in this setup.
Ah. I just left the physical control key alone, and thus have no caps lock key at all. Seems some applications grab the keypresses at a lower level than where PowerToys changes it, so sometimes caps lock is activated when my intention is to hold control.
Was screensharing with a react native hotshot yesterday, and felt my perceived age doubled to 102 as I suddenly was yelling in all caps, with no quick exit.