Will upgrades through the App Store still work correctly using this method? I feel like at one point there was some debate regarding that aspect of the process.
Provided you have purchased it through the App Store you should still be able to upgrade as the purchase is linked to your app store ID.
I did a clean install on a MBP and an upgrade on an iMac. The GM shows up as installed in the App Store Purchased tab on both Macs.