When they say they are happy to flash, what do they mean? Just an off the shelf map such as APR, Revo designed in stages? Or will it be a custom map?
Reason I ask, before you jump ship is, if they are offering you an off the shelf product like APR or Revo etc... chances are the whole injector quest will be short lived, due to the scaling of maf to injectors etc... If its something they know what they are doing and are able to read various points of the maps, adjust the various maps etc... then I would say the injector etc modding you can do.
If its an off the shelf product you will be very limited on your tuning route. The ME3.8.x is a beautiful ECU and very capable, look at its older predecessor, such as the 3.1 found on BMW's, very tunable as well.