They have ways to do that. You would have to check with the store.
Also, this doesn't mean that if your friends are using Windows 10 home or pro that they won't be able to install Appx packages. They can. Seriously, it's just a zip file with a manifest. On home/pro and up, users can install Appx packages by double clicking them.
Only Windows 10 S has the restriction that all software installs have to use the store. The thing to watch will be the way that Windows 10 S actually maintains performance and security in ways that the other versions of Win10 can't. As long as users can install services or device drivers as part of an install it's always going to have the same problems.
For something to change it actually has to change. We all know that Windows installers do dumb sh1t. Appx packages run with the same performance and have the same power as normal win32 apps. The only thing they can't do is modify the system in dangerous ways.
Also, there is an Appx for Servers that is being used for Nano server. It does allow service installation and more serious modification of the system...because it has to. It's still a great packaging technology even if you don't use the store or other elements of their plan.