Emphasize the positive-- you really like the company-- and de-emphasize the fact that the current position isn't a perfect fit. I'd send an email something like this
Mr./Mrs. Recruiter-
I've really enjoyed getting to know the Foo Team and I'm looking
forward to my upcoming interview. During this process, I have come to
learn a lot about Company Name and have found myself very interested
in its mission/ ethics/ technology/ whatever.
I notice on your web site that you have several other open positions
that I think I would be a fit for- List of Positions. Would it be
possible to put me forward for these opportunities as well in case the
Foo Team position doesn't work out?
Thanks,
Your Name
It's certainly possible to wordsmith the language to indicate your relative preference for one role over another. But I strongly doubt that it would matter much. The recruiter is going to spend far less time and effort parsing the language you use than you're going to use writing it. Recruiters find people to fill openings-- they are very unlikely to care much whether you fill a Windows developer opening or a Linux developer opening. They know that there are many applicants for every position so even if you're a great fit you might lose out to someone just slightly more perfect.
It's conceivable that the company would come back and ask you about your preference just so they don't end up bidding against themselves but most companies are pretty accustomed to handling cases where an applicant applies to a couple of openings and two different teams want to make an offer. If the recruiter does ask about which opportunities most interest you, I'd be a little careful about saying that you prefer the Linux position until you've had at least an initial interview with that team-- there may be differences other than technology stack between the teams that you're not aware of. But I wouldn't worry too much about crossing that unlikely bridge unless and until you're asked to.
