I think it is mostly our tendency to humanize everything that has somewhat of a personality.
Making machines have a programmed personality makes it easier for people to work with these, but we should never forget that machines are not really persons.
You know I've watched enough sci-fi to know if the toaster asks "Does this unit have a soul" the answer is yes, PERIOD.
And yeah.....Victor's my boy. Although House uses him like a thing.
But, if I were to give credit to Bethesda, and I don't because Emil is a fucking idiot, the lore seems to suggest the Gen-3 synth project was a TOTAL failure. If the synths as per Fallout 4's shitty writing, compared to Fallout 3's way less shitty writing are indistinguishable to ALL medical tests except the part in the autopsy where you pull the whole brain out, then the synth component, the thing that makes these people a "synth" it's a processing unit, it's a machine brain interface where basic facts, memories, and subconscious conditioning can be implanted wholecloth and also makes them susceptible to recall codes. Gen 3's are fully human, and the synth component is there as a control chip.
The synth component is a fig leaf that allows the Institute to sell the notion they are androids when in fact they are test-tube babies kinda like the Clones from Star Wars only with just the sperm being the actual cloning thing, the growing tube being that horrible red pool and the inhibitor chip allowing them to be made fully grown as they can be implanted with basic skills without the need of a conventional childhood of any kind.
If they stuck with Fallout 3's lore then it would be more of a classic debate...but it's not. The body is human, the brain is human. What the Institute is really saying comes right out of CS Lewi's Abolition of Man, Mankind can be redefined because HUMANS ARE MERE MACHINES, and only the right breeding (upbringing, for now) can make a human anything more.
That's why the Institute is so hideously evil. They are men so completely without chests, so spiritually vacuous, so secular they have become apes in suits (labcoats in this case) who cannot conceive of anything outside vulgar materialist parameters. Everything, including their bodies and their fellows, are the clay, and they are the potters, their own patrons, a law onto themselves.
Morally speaking, it's hard to make the case not to kill everyone in the Institute. Not blow up the place, but kill every last human being in that wretched pit and give it over to....someone who can make use of its resources.