I remember the rule was no more than one *fast food* shop in any given meal period, so if you had two fast casual shops, or two coffee shops, or two restaurant shops, or a combination of two non fast food shops, that was okay, as long as there was at least an hour between them.
That was when their job board did not allow you to assign yourself more than one fast food shop for the same meal period anyway. (I'm not sure whether that feature of the job board has changed. I'm just saying...) Rules might have changed, so it's good that you discussed it with them ahead of time.
The thing about MF is that they arrange a lot of their big bonus shops by phone, unlike other companies, which make such bonus arrangements through a series of emails that leave a paper trail. I guess they figure that if you receive a confirmation email that the shop has been assigned to you at a higher fee, that's enough.