Update: After fast travelling a bit and using the workshop on the un bloated save it went up to 58 megs (from 44MB to 58M
again in no time, also I disabled the ESP Explorer 's esp and now my scripts went down to 11, but the save size incremented a lot after literally just 30 seconds loaded in to fast travel and scrap something then re saving at sanctuary's basement.
You can see, no more Workshop spam though. This is the save that didn't start with Conqueror but still has the esp enabled on it.
So my guess is I did have the Script Backup issue when Conqueror came out, but didn't get cleaned up when I installed Hotfix, also im crashing a lot on that save every few minutes after doing stuff/ fast travelling, I guess due to the number of scripts that are stuck?
One thing I did note this new playthrough with Conqueror enabled, was that Raiders/Gunners/Minutemen/Settlers really anything that was an NPC was not de spawning from the world when killed, causing it to even refresh contents in their corpses sometimes, and the workshops slowly stopped producing stuff, I thought it was a problem with the mod : "Uncapped Settlement Surplus" so I removed it using the mod's uninstaller then disabling the esp as the author specified.
I haven't tested much yet after that because the save keeps crashing after a few minutes all the time but as far as I've went through it workshops no longer spawn in resources like food, caps, water , etc.
The max number of Active Scripts i've seen in Save #1 (Conqueror's save) is about 285 active scripts, it seems to lower and increase randomly, or depending of the area i currently am in, however even in Sanctuary's Basement / Homeplate im still getting a minimum of 190 active scripts in Save#1 as seen in picture #1 which is inside Homeplate with nothing built on it/ no mods modifying that particular cell.
I also went ahead and removed a bunch of mods that appear to conflict with SS/Conqueror using the same workshop scripts (workshopnpcscript,workshopscript etc.) I ended up removing :
Far Harbor Story by Seddo (modifies workshopnpcscript)
BoxHouseAppartment which is a mod from loverslab that places a workshop in the sanctuary penthouse area (modifies the workshopscript.pex)
I'm sure I removed a few more, but no matter, I made sure only Sim Settlements was using that data in MO2's Data tab, this fixed Workshop Framework but not the Active Scripts :/