I use the insteadOf git config option to alias a few remote destinations.
[url "firstname.lastname@example.org:catchamonkey/"] insteadOf = ghc:
which lets you run things like
git clone ghc:language-spec, which uses the full url instead of your alias.
If you have that set, and then use the “Open on GitHub: Branch Compare” Atom command, it tries to use the alias instead of the full url, resulting in an attempt to open
Maybe the Branch Compare command (and any similar) should not use these aliases?