While the hub was down I read some stuff on the Discord saying that it was indeed Questing Bots causing this, it's AI Limiter was mentioned but then again Performance Improvements mod was also mentioned, so who knows for sure. DanW is aware of it and with 3.11 just released I'll just wait until all my mods are updated for that.
I tend to only slightly increase my raid times, i.e Customs/Woods/Shoreline to 1 hour and I experienced an invisible scav in Fortress about 20 mins in so I don't think it's caused by longer raid times, seems more like generation errors. I also don't use AI Limiting in the QB F12 menu and use QB spawning. I also got frozen PMC's at extracts twice, on Customs and Woods which you don't mention, lol, so I dunno at this point. I'm very careful with my install and rarely experience issues but 3.10.* has been one iteration I won't miss, really had to force myself not to go back to my 3.9.8 install. No reflection on SPT though, all the performance issues and jank was purely on BSG, polishing a turd is no easy feat.
Anyway, patiently waiting for 3.11 mods to release is my new quest.