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Good question, although many devices support dual PTP and USB Storage modes so if they don't support exFAT, there is always alternates. I wonder if there is a move to exFAT and demand increases whether Apple is willing to sign agreement or whether the existing agreement with Microsoft covers such technologies.

For Microsoft I have a feeling that they're more concerned about getting money than whether or not a particular operating system uses it. If There is a requirement to pay for licence then it helps Microsoft in the long run. It helps them by raising the required sales price to cover the licence.

Lets say that Red Hat bites the bullet and says, "we need to create a Linux desktop with all the trimmings for customers". Part of that would involve licencing a huge swag of technologies off Microsoft. By the time Red Hat got through with licencing all the technologies required for a fully feature desktop operating system it would probably add another $30-$40 onto their operating system. Couple that with the need to recoup the intial investment for the product and it would probably raise Linux to the same price range as Windows thus killing off any possible intial cost argument relating to Red Hat being lower cost than Windows.

So I don't think it is as simple as Microsoft trying to tie the hands of Linux distributors when it has more to do with raising the cost of Linux to meet the same price as Windows. Then from there it is easier to argue that, "both are the same price, but ours is superior compared to right now where vendors can always fall back on the "but we're cheaper" argument.