As I understand it, Apple will be making most iOS apps available to Macs with Apple silicon automatically. I don't really have any issues with this in particular, since I don't have a Mac app right now, but I was curious if this automatic process would have implications in the future if I wanted to offer a full Mac application myself (either using Catalyst or native macOS frameworks). Would I be able to pull my app off the automatic program and make it available in the Mac App Store at that point?
Converting an iOS app available for Apple silicon to a Mac app
Yes, you will be able to pull your iOS app from macOS distribution. With regards to WWDC 2020 video "iPad and iPhone apps on Apple Silicon Macs" you will be able to uncheck the "Make this app available on Mac" check box for your app in App Store Connect.