Thanks for the info over the ticketing system. I thought I'd update this thread to clarify it to everyone else.
The file action entries will only appear for local or 'direct' server storage. FTP or any of the Flysystem storage points are deleted straight away (sorry I should have mentioned this above!).
In your case you have 2 servers, 1 local, 1 Flysystem FTP. I uploaded an image, it appeared on the local server, I deleted it by the users account and it appeared in the file action queue fine. If it was stored on the FTP storage point it wouldn't appear in the queue.
I guess there's an argument to say these storage points to act the same as local/direct storage, i.e. move the file into a _delete folder, then clear via the action queue. I'll add a note in the RFCs to review.