That sounds like a reasonable diagnosis.
CM is generally bad at raising the proper events when it acts with one of its cheats, like instant blueprinting or instant deconstruction. In fact, instant deconstruction likely makes the problem worse because both Autobuild and CM will get the event that an entity was marked for deconstruction, and Autobuild will make a record of that, and CM will instantly destroy the entity but not raise an event. So either way Autobuild storage just continually increases.
Mooncat hasn't been around since 0.15, so I'm not expecting it likely that Creative Mod will get any updates to make it play better with other mods in these sorts of cases.
Autobuild does clean up its storage, removing entities that no longer exist because something like CM has silently destroyed them, but only when actually trying to do automatic construction or deconstruction, i.e. when it's enabled and the player is stationary for a while. I'm guessing that when you're experimenting in CM you don't have the Autobuild toggle active, and/or aren't lingering with the character near where all the instant (de)construction is happening. I could actively sweep even when the Autobuild toggle is disabled, but that has UPS costs. :(
It might make more sense to just mark Autobuild as incompatible with CM, but it means you'd have to change your set of active mods when going back and forth from your creative mode maps and actual gameplay where you want to utilize Autobuild.