The royalty that Samsung is paying Microsoft per Android device is unknown, but earlier this year Microsoft secured a similar deal with HTC where it gets $5 per Android device sold. With Samsung and HTC under its sway, Microsoft now receives royalties for over 50% of Android sales in the US; only the soon-to-be-owned-by-Google Motorola Mobility remains.

That resolution alone should be more than enough to send a shudder up Big G’s pant leg and across its jockstrap — but to add insult to injury, Samsung announced yesterday that it is now working with Intel on Tizen, a free, open-source, Linux-based smartphone OS. It will be derived from MeeGo, the critically-acclaimed but stillborn OS that itself was a merger of Intel’s Moblin and Nokia’s Maemo operating systems.

Now… why would Samsung sign an Android licensing deal with Microsoft, and then partner up with Intel on an Android-competitor OS? Could it be that Samsung only agreed to pay royalties to Microsoft because it foresees an Android exit strategy when Tizen is complete?

Paying a royalty is one thing, but Android OEMs can’t be comfortable with Google’s acquisition of Motorola Mobility either. Google already plays an odd closed-open game with Android’s source code, too — something that certainly won’t improve with Motorola becoming the “first party” Android OEM — and, more importantly, manufacturers that want early access to the source must agree to submit all of their changes to Google for approval.

Tizen will be a fully open OS hosted by the Linux Foundation, and steered by Intel and Samsung; very similar to how Mozilla runs Firefox. There won’t be any “hidden” branches, and OEMs (including Samsung) will be free to modify the codebase without having to appease a commercially-conflicted third party. Samsung could quite easily make Tizen look and feel like Android, too, and with some licensing deals it might be able to run Android (Dalvik/Java) apps. That’s the thing with Android: in essence, it is an open source project, and beyond the developer support provided by Google, there is no intrinsic reason for Samsung to stick with it. All of its functionality, look, and feel can be replicated — and in the process, it can waive the royalty it must pay Microsoft, and gain oodles of maneuverability.

Meanwhile, of course, we must not forget that Intel is Tizen’s co-founder — and Intel would absolutely love Samsung to build some phones around its upcoming SoC Atom chips…

Read more at Microsoft on the Issues and Tizen.org