The problem that could occur is: Right now Microsoft doesn't care about Linux or competitors, every OEM has to buy a Windows key anyways regardless. If SteamOS actually becomes a shippable option, Microsoft's cavalier attitude is going to change quickly, and a lot sooner than it will take them to get an Xbox Handheld out the door.
It's in their licensing, and how MS-DOS became the de facto operating system of early PCs. If you want to license Windows, you have to pay for every unit you sell - not just units with Windows pre-installed, but every unit.
The deal Microsoft does with OEMs gives them a discount only if they pay Microsoft for every PC they sell, whether or not it actually comes with Windows.
I don't understand how that's a problem. Can you go into a little bit more detail about what you think the consequences might be to manufacturers choosing to use Steam OS or some other Linux operating system on their handheld devices?