I don't think it's unreasonable to have an aftermarket RMM and still want to be eligible for the TSB.
Ford has acknowledged through the TSB that a problem exists, and the fact that an owner was unhappy with the RMM and replaced it prior to Ford ackonwledging the problem, shouldn't 'disqualify' you for the TSB.
If I had replaced the RMM on my own dime, I would just explain that to the dealer and if it was a problem for them to perform the TSB, have them go to the regional guy for approval.
I don't think there is anything unreasonable about having an a/m RMM and getting the TSB performed.
You fixed a problem Ford refused to fix, and Ford's subsequent TSB shows that you, the customer, was right and in no way should be penalized for Ford's 'late admission'.
Like anything else, being reasonable and discussing it like a human, not an animal, should resolve any issues.
If a dealer gave me a problem, I would keep going up the ladder til I got satisfaction.
edit: This is also why I let my dealer change my oil. They get to know you, you're not just showing up to b**tch and moan.
It's much harder for them to treat you like a # if you know them and have a '2-way conversation'.