The Stars Align
There's been a waterfall of events that I think is leading us to this moment. First, take Microsoft: they don't have an offering right now. Windows mobile was just sent out to pasture, their Lumia brand hasn't had a new phone in almost two years, and OEM support for Windows phone was never strong. Changing the strategy a bit, CShell promises to package full Windows 10 to a screen that fits into your hand (which may be rotated 90 degrees from normal windows). They've also released Windows 10S - their operating system that will install apps only from the app store. Finally, they announced that starting with the Snapdragon 835, full Windows will come to cellular mobile chips.
At the same time, we're hearing that the Surface mobile device, whatever that will end up looking like, is still a distant device. It will revolutionize the mobile computing world, but it's not ready for the mainstream yet. This has a created a gap for Microsoft in the mobile market. The Samsung, though admittedly halfhearted, would be a way for Microsoft to a) have a device for the diehards and the enterprise users, b) hype the market for their OS, and c) show investors they haven't abandoned the space. At the same time, we've seen Samsung doing its best to gain more ground in the enterprise market with Knox and DeX. Microsoft and Samsung have shown the enterprise market they are working together on the Continuum-like DeX by Samsung showing off how well the Microsoft Android apps work on a large screen, and in return, Microsoft has been selling the S8 and S8+ in their stores.
All the pieces of the puzzle
Samsung is also up to speed with Microsoft's favorite input method - the pen. The Galaxy Note line has been a big screen, pen housing phone since 2011 - over 6 months before Microsoft announced the Surface Pro for Windows 8. With the first and second creators updates, we're seeing Microsoft put more emphasis on Windows Ink and the stylus input. It's clear that both companies have also been working together on this technology with the release of Samsung's new line of premium laptops and tables running Windows 10 and all sporting S Pens and Windows Ink capabilities. It's not hard to see how these companies have complementing values and beliefs when it comes to pen input and it would make sense that Microsoft would want to have Samsung's device represent its newest mobile efforts and capabilities.
The relationship and tools exist
And it might not be something they'll ask Samsung to do at the factory. Some of us will remember a time when Microsoft worked with Xiaomi to release a custom Windows 10 mobile ROM for their Mi4 Android handset. There were rumors that they had built one for the OnePlus 3 and a handful of other devices as well. It is well withing the realm of possibility that Windows simply wants Samsung's blessing in releasing a ROM for consumers to choose. Or they could be asking Samsung to install it at the factory. I would guess each company wants the other to take responsibility for it. If it happens, it will be interesting to see how it works.