Danny,
Certain operators DO have an issue with number of FTO's attended. Flybe being one of them for example. In their recruitment campaign earlier this year it was clearly sated in the application process that they preferred applicants to have attended only a limited number of schools. I cant quite remember what the exact wording was though.
As for cost, fibod makes a good point. If you stick to the one FTO for CPL/IR and MCC you might get some discount. I've seen a number of places advertising free MCC if you do the CPL and IR with them. Worth considering, you could certainly save a few grand.