What's the difference between Unity3D's Windows Store build and PC Standalone build?

I want to use a Microsoft Surface 4 pro to test my app built with Unity, I can see there are 2 options, either through Windows Store or simply make a PC standalone .exe file and run it on the device.

My question is will it make a difference in terms of how touch inputs or any other aspect of the app are handled?

Thank you,

.NET 4.6 support for what I see. Though the editor can’t cope with 4.6.
And you can’t simply put your app out there with a Windows Store build.