As far as I'm aware., AppGameKit actually runs the Application from a Temporary Directory: System:\Users\[Username]\AppData\Local\AGKApps\[YourAppName]
The result of this is that you can still Modify the Installed Directory version., and it will Shadow it to this Directory when you next run the Application
Yes, updating the Bytecode.byc will update the AppGameKit Script (i.e. what you've written) but remember that the AppGameKit Player embedded in the Runtime is Dynamic; including ONLY the Packages that you've used Commands from.
This means if your Bytecode.byc suddenly decides it wants to use Audio when you never used said Commands when you first compiled; then it will simply crash the Application with a Runtime Error.
A way around this is to deliberately use a Command from each Package; but unlike DBPro this isn't quite as easy as AppGameKit doesn't have a clear list of Package Libraries.
As best as I can tell the Help Sections seem to coincide with it, but don't quote me on that.
You'll actually find A LOT of Apps nowadays don't patch themselves... as Steam, Microsoft Store, Origin / EA Launcher, etc. well they all have built-in Delta Patching.
So unless you're planning to Self Publish, chances are whatever platform you intend to use will support patching outside of the Application that will perform automatically when you add a new Patch.
In-fact with Microsoft Store, when you add a new version of your Application Package; it will automatically generate the Delta Patch for you and push it out when you enable it on the Developer Account.