I just ran into this, too. Any luck on your end? Did you contact App Store Support? Hopefully this is just a temporary glitch as Apple rolls out the Universal Purchase functionality, and not a new requirement to bundle the apps as a universal purchase.
I contacted Apple Developer Support, and the representative actually told me to put a space at the end of the name of the Mac app to make it slightly different from the iOS app. Surely that's not an official solution. I've replied three times to clarify whether this is an intentional change on Apple's part, or a temporary bug in App Store Connect, but he won't answer directly. He says the names must be different, which implies this is a new policy, but he won't acknowledge that this was supported two weeks ago or explain why it changed.
FWIW, I released my Mac app with an X at the end, like "App Name X." It's meaningless, but at least it looks intentional, rather than putting a space at the end, which would just look sloppy.