I don't think you could setup a foodie tour in either place.
Problem is that in Ambon you will find good indonesian/Malukkan food (Smoked tuna, Kenari almond sauce, etc. and even excellent coffee & snacks at Joas ) downtown Kota Ambon, depending where you stay it can be a loooong way from your place. (Note that Ambon is one flight/ferry transfer from Banda islands, This is the best spot for culture and food in Indonesia IMO)
Some Dauin upmarket resorts will serve good food but westernized , otherwise I find that local Filipino fare is kind of bland, I would add some exceptions for Kinilaw (raw fish -preferably tangige/spanish mackerel- in ginger, chili and lime juice) BBQ'ed pork belly and... mango pancakes.
Personally I thought globally Ambon (3 trips in Ambon) has an edge on both macro (more diversity than Dauin) and coral dives outside the bay.
Kota Pintu/Hukurila caves are magnficent and if you can find an operation located south of the bay that goes out to Lease islands there are some really good blue water/coral reef dives.
That said everything is easier and more laid back in Dauin (4 trips in Dauin so far).