Just charge a flat rate that will always make you a profit no matter how many attempts. Anything else is just asking for needless drama. Commissioning an item isn't cheap, if they want cheap and don't care about the model then they can go buy whatever shows up on the AH.
You do realize since success is random, it could take an infinite number of attempts, so there is *no* way to charge a flat rate that will always make you a profit no matter how many attempts?
That being said, I'd probably go with 10x CoM. (cost of mats) Though if it's not a rush job or I already have 10x parts on hand I'll figure CoM as the mission cost of mats. (if it *is* a rush job and I don't already have 10x parts, I'll use current minimum market price to reach 10x mats)
I'm not really sure I feel comfortable using the prices displayed on the GTN as actual prices things sell for under normal circumstances, as if they're on the GTN they haven't sold yet. And the prices are so high except for serious rush jobs, I can't see anybody actually paying them when they can get 'em from missions for MUCH cheaper.