You can add in a fake religion, give it the house flags with random=yes, then use it to customiser yourself those flags in game (as with the in-game dynasty editor you can use any religions flag.)
But CK2 doesn't like flags of the wrong religion, so probably everytime you load a save, you'll have to do it again.
And they can't be of the right religion, as then random baronies and random characters would get them.