Portage should not notify me if I am using these options...
I can't reproduce it, and this really sounds like a PEBKAC. Please note that repoman silently ignores incorrect options and your stabilizations suggest that you aren't using '-d', so you probably have typo in there somewhere.
'repoman --include-arches arm64 -d full' seems to be fine. As you stated, I most likely had a typo when I filed this.