1) I don't think any of these plugins are unusual but here's the list. The top one isn't actually installed:
2) I use EmuMovies but I'm not sure that qualifies as a third party scraper. No other unusual tools for metadata collection.
3) Launchbox Version 13.15
4) I noticed the file size jump last night when Launchbox was initializing meta data but I only watched it happen that once. I spent several hours last night deleting duplicate entries and was able to get the file size down to a reasonable amount. It was helpful that most of the bloat was in relation to a handful of games (like 1,000,000 lines of code for Wonderlands controllers) so it was manageable but not quick. Since finishing that process, I haven't noticed the file size jump again.
A few other notes:
My installation is admittedly a bit unusual in that I have Launchbox/Big Box on my PC and my Ally X. I use Syncthing to keep the installations synced. That being said, I don't know why that process would have affected the contents of this one file. When Syncthing has an issue with syncing a file, it creates a duplicate with "sync-conflict" in the name, noting that there was a problem with the file during the sync. I haven't seen it alter primary file contents in any other use case.
Last week, I did complete a multi-week effort to hand-curate all the thumbnail art, box art, background art, and logos for all the games in my collection. I have about 340 games imported (over 120 of which are Windows games) which isn't a small amount but it's awfully meager compared to some folks' libraries. That process had me closing down and opening Launchbox repeatedly. I also cleared the image cache within Big Box often during the work.
I did actually take a backup of the bloated file somewhere around the 3 GB marker, if you'd care to take a look at it, we can figure out how to share that if necessary.