It's a shame though, because the potential of this mod is very high. After doing so, loading the save, saving again, and then re-analyzing with the tool I find no more messages about bloat data.
It apparently was able to remove all remnants of the mod in my newest save - I did two things: 'Remove Unattached Instances' and 'Remove Instances with Undefined Classes Only'.
After deactivating, I used a program called Savegame Script Scalpel (on the Nexus) to remove leftover savegame bloat.
