The issue was found to be enemy expansion "distance". The lag would happen regardless if the setting was enabled or not, as long as it was enough for the biters to attempt to cross a chasm. The stuttering will become more intense as the setting is higher, 20 being severe, and 10 being barley noticeable. Since this is more of a Factorio Base issue, this thread can be closed I guess. Although, I would suggest Enemy expansion distance for players to be set to an absolute minimum, to avoid late game stuttering.