From what I've read, it sounds like the interoperability issues come from not implementing AP the same way as Mastodon rather than anything specifically protocol-related. Hence, e.g., Pleroma going out of its way to be Mastodon compatible as a design goal and GoToSocial having lots of issues because it hasn't yet gone that route[1]

[1] e.g. they have an issue where some client apps don't work with GTS because GTS doesn't advertise a version number sufficiently high enough - because the apps are looking for "v > 2.10 because that's when Mastodon introduced feature Z".