I don’t think that last part is necessarily true. I did the Moore Mafia flash and they did adjust fuel maps according to the mods you tell them you have as they will select a profile from a bike they dynoed with similar mods.
Yes you are correct: the key word quoting your message is "similar mods".
Every bike is made different. Even same year, same model bikes may have sightly different engines due to production tolerances and break in procedures. If you add mods on top of that and location you are getting an even bigger gap.
Point is: do this "big name" flashers have a tune available that will improve your bike's tuning? Yes
Will it be perfect for your bike? No: there will be an error due to engine tollerances, break-in procedure, mods, sea level and weather temperatures. A bike that is rode in Florida will need a different tune than a bike that is rode in Minnesota.
It's definitely better to have one of this mail in flashes than no flash at all but getting your bike a custom dyno tune that is specific to its engine and mods and the region your riding in will always be the best option.