they are not native, they are just as separated as other apps, the difference it's you can't uninstall unless you run powershell commands. only some really system apps could have problems. but what I did when I removed Edge was to remove the folder and sfc repaired, Edge was working good, but I wanted to test it.
sfc reported any error it couldn't fix? if it says something couldn't be fixed you could try dism.
but like I said, you can always go to powershell and uninstall the apps like mail and calendar that way. and then go to store and redownload them. of course you should fix first the store. so there are some ways you could try like reinstalling the store.
you can get all the packages names by Get-AppxPackage -AllUsers
and reinstall the store that way.
Add-AppxPackage -register "C:\Program Files\WindowsApps\Microsoft.WindowsStore_2015.8.25.0_x64__8wekyb3d8bbwe\AppxManifest.xml" -DisableDevelopmentMode
or you could reinstall all apps by using
Get-AppxPackage -AllUsers| Foreach {Add-AppxPackage -DisableDevelopmentMode -Register “$($_.InstallLocation)\AppXManifest.xml”}
I restarted my computer and ran the command right away so no apps would get locked and give an error, that's a tip that worked with me.
you could also try to do something extreme, make a system restore point thing, and delete store from program files\WindowsApps and run sfc, it should be reinstalled since it's a system app, it should be like when I deleted Edge and sfc fixed it.
But of course this is risky.
Everything works great on my side after many tests I made, there is no much I can't say about Store, maybe a driver not installed could be the cause? or something? who knows, it's not my computer. but nothing I have suggested would destroy your computer and make it useless so you could try it. I have deleted and reinstalled apps and such, even edge. and I am still fine using Edge here.
anyway, if you get to fix your Store you could always run Get-AppxPackage *windowscommunicationsapps* | Remove-AppxPackage and then download the apps from store.