This bug is actually in the rpmautospec integration in fedpkg/rpkg (which I contributed there 😊):

...
         # See if this build has been done.  Does not check builds within
        # a chain, or if the %autorelease macro is used.
        if (nvr_check or self.uses_autorelease) and not scratch and not url.endswith('.src.rpm'):
...

The conditional clearly doesn’t implement what the comment above says. I'll submit a PR with rpkg.

NB: as I understand it, the only way Epoch contributes to your issue is that fedpkg/rpkg only checks if the same N-V-R already exists as a build in koji.

NB^2: You shouldn’t bump epoch to address incompatibilities introduced in a minor release, only if the package otherwise can’t be upgraded, see https://docs.fedoraproject.org/en-US/packaging-guidelines/#_use_of_epochs

I recommend removing the Epoch from the spec file (there doesn’t seem to be a built package with it yet), even though this will throw off the rpmautospec release counting algorithm. You can work around that by using %autorelease -b 2 (which starts counting releases from 2) and reverting that on the next version bump.

I've filed the pull request which should fix the issue as rpkg#640.

This has long since been merged.