Just ask and be nice about it. (See my comment on these questions in the comments below.)
... (preferably a custom-build by myself) Linux PC instead (for "the same cost")?
The price of the hardware may be the same, but you can't make the assumption that the costs will be as well, because price and cost aren't the same thing. You're going to have to spend time building and administering your system, and if the rest of the company isn't using the same tools you are, there will be time spent dealing with compatibility issues.
Unless you're so good at what you do that the company thinks the value of your work eclipses the costs of having one oddball system in the office, they may simply say "no thanks" and move on to the next candidate. If you stand on it too much, I can almost guarantee that the phrase prima donna will be uttered at some point when everyone sits down to discuss whether or not to extend an offer.
If I can relate a personal story:
Last year, I received an offer from a shop where the standard desktop/laptop is a MacBook. My primary working environment has been some non-Mac form of Unix for close to 30 years (20+ of those with Linux). Like you, I've got everything customized in a way that I find productive and didn't figure it was going to be particularly pleasant having to give all of it up. The job was attractive enough that I decided to take the plunge, and one week before my start date, a MacBook arrived at my door which was fully configured with all of the company's applications, remote backup software, VPN credentials, etc. It was a bit awkward at first, but within a couple of weeks, I had my MacBook doing 95% of what I have Linux set up to do right down to the keystrokes. The other 5% has been chalked up to broadening my horizons.
What I learned from the experience is that pretty much every desktop feature you can find on one platform can be found on the others if you look around a bit. That includes tiling window managers.