Related CLI and GUI applications with same name?
Not sure how to understand how there could be a conflict in such cases:


foo.app is a directory (usually within /Applications) which contains all the files relevant for the application to run (including any resources, translated texts etc)
foo is a binary installed within foo.app which can be called from a shell by specificing the path, symlinking it from /usr/local/bin, or using any other way available in shells


So this are differently named things of different types, there shouldn’t be a conflict as far as macOS is concerned. We can‘t know what the App Store Review will make of it.