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.
aMASE
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Ipad apps will only be available automatically and run ”as-is” on ARM Macs running Apple Silicon. For Intel Macs you still need to recompile with Mac Catalyst.