That's a false equivalence and changing the argument/moving the goalposts.

You asserted they'd eventually consider humans with mutations worth exterminating. Eventually means they do not yet do so, as if that weren't readily apparent.

Then for proof of this, you show how 200 years and 400 miles later a 3rd generation descendent of Maxson orders a trusted lieutenant to be terminated when it is discovered that he is not human.

Not being human =/= humans with mutations

inhuman infiltrator who admits they cannot trust themselves or their thoughts and memories =/= humans with mutations

If you want a clearer example, look at how the Sole Survivor is treated by Cade on board the Prydwen when you join the BoS in FO4. He asks about mutations or exposure to extreme radiation, but even so he does not show any desire to terminate you. It seems routine for anyone who isn't raised within the BoS to be subjected to such things. It definitely doesn't keep you from joining, regardless of how you answer.

That's 200 years after the events in FO76. With a direct descendent of Maxson and the original and most strict branch of the BoS of any lore we've yet seen. How long does it need to be for you to consider 'eventually' to have passed?

BoS are clearly authoritarian and clearly not always the good guys but idk why everyone just ascribes any 'bad thing' they can think up as an ideal that is a central tenet of their ideology.