I have noticed that the enemy retreats a lot less in entrenchment (but that may have changed in the original (vanilla?) at the same time.
No they don't retreat a lot less in vinalla now, I come in with a fleet of ship, the enemy AI on normal was twice my size and they still retreat upon entering the system.
One of the major reason i got Entrenchment so I could get starbases, and for a Trekker, the original star trek mod is not longer develop so, I got entrenchment to hopefully continue to play it