I've run into this problem as well.
What you can do is to check to see if there is an update available, then notify your users that they can either wait or update manually (through the Windows Store app, which you can open for them). You can also notify them of the importance level of the update (just UI fixes/additional features or is it a critical security patch?).
Lastly, you can also register the users for toast updates via an Azure Notification Hub, then send out a toast notification about it.
If it's truly critical, you can also include code in your app to do something like lock down unless it's fully updated or something similar.
In my experience, as of right now, these are our only options. Maybe one day they'll allow us to force an update via a Background Worker or something while the app isn't running. As of right now, that's not an option though.