Discrepancies between OneNote 2016 and OneNote Windows Store App

Counter question: There are two Photoshop apps. Photoshop CC for WIn 32 and Photoshop Express UWP app for Windows 10. Why can't they have the same features?

There are many possible answers to your question. From a product political perspective OneNote 2016 is basically a very old program which has not been developed very much since the 2010 version. The WIndows 10 app on the other hand is rebuild from scratch and this is the one the developer team is focussing on.

From a technical perspective it is not possible to integrate ALL functions of OneNote 2016 into the UWP app. For example all the DLL and library sharing (using Office spellchecker or Autotext for example, but there are many many more examples) is not possible with UWP apps, at least to my knowledge.

The Windows 10 app is getting more and more features over time but I am sure it will not be totally par on features with the "old" W32 version (OneNote 2016) at any time. 

In addition it seems that OneNote is moving away from a business productivitiy tool to a more educational focussed app. Except you need glitter ink effects or funny stickers for your daily workflow :) But wait, you said you work in education so the development could well go in your direction.