So I set all city and plot upgrades to manual via the Holotape and MCM, hoping it would prevent crashes and it did help a bit, but I noticed that Sanctuary continued to auto-upgrade their plots. After a bit of digging I noticed that within the Holotape>Options>Gameplay Options>Local upgrades were still set to Auto.This was also the case when starting a new city plan. Yet this isn't the case for some settlements, such as the prebuilt ones I selected at the start of the game (conqueror) all their local>upgrade settings are set to manual. I believe that starting a new settlement overrides the global upgrade settings and uses the default Auto upgrade. Also on a side note, Randomised clutter as a performance option is only featured on the MCM menu and doesn't appear on the Holotape.