I understand that, but with UK's system there are no exit controls, so I assume if I checking in with a given passport it's counted that I exited with that passport? hence the other passport could be flagged as having overstayed?

Or let's say the following ; I enter UK with passport A ; I leave UK with passport B ; then I return to the UK and enter with passport A and finally leave with passport A.

So the issue here will be that I entered UK with passport A a second time without leaving?