The decisive part here, however, isn't the flavor of API call used, but the roles mask. Right now, Remote Buddy is only asking for viewers and editors, but not shells.

I'll evaluate the security implications of including shells here as well and may or may not add it to one of the next versions.

Until then, you should be able to execute .command files simply by installing iTerm (at least the old version I've installed identifies itself as an editor or viewer to the system, not as a shell - and is therefore listed).

Best regards, 
Felix Schwarz