Need new ECM for brand new 2010 Tacoma - Are they model specific?

Long story short...I need a new ECM in the new Tacoma I just bought that I haven't even driven yet. They are putting in the TRD supercharger but the original ECM will not accept the reflash because the brake override recall reflash was already done and apparently the SC reflash is not compatible if done after the brake override reflash. It does work however if done before the brake reflash. The solution to this problem is swapping out the ECM with a new one that doesn't have the brake override reflash done. My question is - is the ECM model specific, or do they just program for specific vehicle configurations? I'm guessing its vehicle specific but I honestly have no idea. Are new ECMs readily available, or is this going to be a hard part to locate? Truck is 6 speed manual 4.0 double cap which is not very common so I have some concerns about the availability of the ECM and my dealer is not giving me straight answers. Any help would be appreciated. Thanks!