Righty, further testing has resulted in catastrophic failure. The nozzle guide has snapped off.
A worn mag catch was allowing the mag to pitch causing the nozzle guide to occassionally bite into the charging handle. Up close what I thought was just normal wearing in on the charging handle definitely wasn't. So that's a new catch, bcg (stripped threads) and handle. Why does it have to be this way VFC?
The bolt being angled could explain why it was struggling to do those last 2mm. Confusingly, this still happened without the mag in, perhaps the bcg or charging handle have deformed due to the excursion. Luckily the upper doesn't seem to be worn. I will take another look at the hammer, thanks for the tip.
In testing I took the front off the upper. Nozzle out of the bcg mates with the hop and receiver extension fine, back in the bcg everything is flush as well.
The mag catch was always very fussy, hopefully this is fixable!