That’s something that’s usually outside the HR purview. (And there’s some good reasons for that. Namely maintaining the integrity of their confidential data.)
If they’re not already using Linux environments; and to be blunt, they’re probably not unless you’re specifically being hired for dev in Linux-world… then you just disqualified yourself.
Even if they do allow it, there’s probably going to be times they really need you in windows, and they’re now going to have to weigh how common that will be and if they want to tolerate it.
So, you need to ask: are you willing to hold out for that one company; for that one job, that may never come. Are you willing to take a potential pay cut?
I get having standards, but, they also get to have those standards and they might just pass because you sound annoying.
You can always decline an offer, you can’t accept an offer that’s never made.