Let's assume, for the sake of argument, that Microsoft has a good business plan for their stores. And, for the sake of argument lets suppose that in fact MS would like the store to at least break-even. Other wise they would have to spend a lot of money on the stores to recoup the small amount that they are losing to Apple.
1) Putting MS stores near Apple stores is not a dumb idea. In fact it saves them money.... Apple has done all the demographic research to place their stores. Franchise food operations do it all the time. Burger King, when they were starting up, merely located near an existing MacDonalds. Mickey D's had already identified neighbourhoods where people liked to eat hamburgers (as opposed to those neighbourhoods that liked lobster where neither McD's or BK would sell many 'burgers.)
2) Since the Apple friendly locations have a higher proportion of people who have a higher than average disposable income (whether or not we like it, we must accept that Apple computers have a premium price tag. I happen to think the premium is justified by a system that 'Just works' and that works well)... then the MS stores aren't likely to be carrying cheap PCs. Customers in those retail locations aren't shopping at Walmart.
3) If MS stores aren't trying to attract the price-point conscious customer, then we can assume that the products are going to be higher-end products.... products with a larger profit margin. I don't know which PC makers fit that bill, but it I don't think it will be Dell. Perhaps they will partner with Lenovo? If MS is worried that they are losing market share to Apple in the small business sector, then that is a possible partnership. Packaging a small business solution, and having someone who can explain it in person, could do well - and undercut what I think is Apple's next big market push - Small Businesses who need a small network.
4) Or MS is totally out to Lunch.
the later