I’ve done a file-by-file comparison (not subscribed to any workshop mods). The maps dm_chopper.bsp, dm_crossfire.bsp and dm_rail.bsp (and dm_rail.txt) are different.
I’ve also compared the server maps with the maps in the v0.3.0 update of the main game (from a backup), and they were all byte-for-byte identical, which means the dedicated server was never updated alongside the v0.3.1 patch of the main game.