The risk with Microsoft's approach is that companies will think "our Windows app runs fine on Surface" and invest little on making their application work great on Surface because they form a small part of the market.
The risk with Apple's approach is that companies will think "it's too much work to make a custom UI for such a small market".
I guess time will tell who wins this. Possibly, things will go like they went with Mac OS and Windows: some companies decided to build applications for the Mac, thus forcing others out of the market, and making it easier for them to develop Windows versions. Another possibility is that the way larger market in 2015 vs 1985 and the existence of many existing iOS apps makes more companies decide that developing a custom UI for iPad Pro is worth the effort.