I may be mistaken but, in the fog of my memory, I thought the AI was being modified to not spam single ships and to instead create fleets.  If I am wrong, I highly recommend that you do make that change.  The screen snapshot below shows a large number of single ships being sent my way by the Baratak.  It looks like "The Attack of the Fireflies".  There is no way that they can succeed with this strategy and killing them one by one is a very tedious part of the end game.

Here is a link to a save file on DropBox that will let you see this (they are in the top right sector):

https://www.dropbox.com/scl/fi/gkcz6lmih2t4oavlrbof1/Single-Ships-Under-1.71.495696.GC4Sav?rlkey=lesxy3b56df5b3sl97wwuat0k&dl=0

You might also use this save to check how you are calculating the components of Prestige Victory Progress. Specifically, take a look at the Military Power score.  The Torians and I both have a score of 18, but if you look in the Data Bank at our relative Military Power, I am way ahead.