You, or your company can create whatever apps you need and install them direct without going through the app store. This has already been done so many times for the iPad it's silly.
I will agree with your second paragraph, but you again miss the possibilities with your third; though I will agree that relying on mouse-centric apps is a major part of why the touch UI on Windows failed for 11 years. JJFitz does prove that legacy apps are usable, but I'll agree with you that they're not necessarily the most efficient. OneNote is good for handwriting equations, etc., but I'm not sure OneNote can automatically convert those equations into computer-understandable text where a dedicated math app might.
In general, while it seems you do understand most of the advantages and disadvantages, you overlook both the short-term and long-term changes involved. It's not that touchUI on a desktop isn't practical so much as the desktop's form factor isn't practical for touch; you need to bring the display close enough to make touching it easier and yet still leave room on your desk to use a real keyboard when necessary. The mouse is now obsolete; it's just a matter of time before it disappears entirely.
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