Thanks for trying. I appreciate the effort even if there isn't a solution. It's like every object created in a settlement gets the keyword reference added to it.
I don't suppose there's a way to see active scripts and overrides like there is for objects in the mod files that you know of? i.e. what scripts are active on a workbench and where did they come from?
Crops definitely have the link and also lots of other things like planks, turrets, chairs, etc.
Anyway, I tuned the keyboard macros up reasonably well and removed the persistence on all of those deleted items and most were immediately removed; i.e. "(00000000) is no longer forced to be persistent". That got my save down from 100MB to 82MB so that helped.
I'm not incredibly enthusiastic about deleting the entire thing and reinstalling Steam, Fallout, and all those mods but I guess that's the only alternative to periodically cleaning up the objects.
If I could figure out what makes them persistent maybe I could script my cleanup but forced persistence which continues after the linked reference is removed is only a thing with placement commands I think. Just the console has an explicit force persistence toggle which is odd. Also, some of the changeforms for deleted objects had no workshopobjectscript but most did.
At any rate, unless it happens to other people I guess this is a "closed case" since it's probably some outside influence on your mod's action rather than the mod itself.
Again, I appreciate the help!