There is nothing on the 03 mondy that I can think of that would need coding to the engine, but I will check, so as you say it should make no difference what ecu it has, diesels are another matter as pumps can be coded.
At the end of the day they took the job on, so have got a cheek to even think about charging as they haven't done what was agreed, unless you told them it doesn't have to run, , let me do some checking and I'll get back to you, I'll ask me mate as does does ford warranty work in essex on the lecky side of things.
tabetha