Which Mutants do BOS seek to kill that everybody else doesn't?
They have no history of killing non hostile mutants, unless you can point out any evidence of this......and the sole reference to them shooting (but not killing) non feral ghouls in F3 isn't really it. There is no canon history of BOS killing non hostile mutants despite it being trotted out on a regular basis.
They try to kill a Synth Infiltrator, so yeah not really a sign of them killing non hostile mutants and frankly at best banishment is the best option for Danse since he can never be trusted since he can be turned off and reprogrammed by the Institute at any time.
They can through the feeding the troops buy, charm, intimidate or kill the already established settlements for their crops. I see nothing wrong with the locals contributing to their defence, just like the NCR who expand in the same manner. The player decides how or even if those events happen.
Historically they have taken weapons tech (generally energy weapons) from locals and scavenged the rest from other locations however in this game there is not a lot of examples of BOS 'stealing' tech.......I think they try to take the MM artillery in the MM ending, so again weapons tech. Aside from that all the tech seems to be taken from hostile groups.
Yeah thankfully the para military charity has ended, but given the state you find them in F3 that should really be a good thing, however EC BOS is still recruiting from the locals and helping them by exterminating the hostiles that plagued the locals. EC BOS has simply taken the logical step of taking control of the region if they are going to be defending it.