So basically, suck it up and manually rearrange macros for every group?

And I'm not sure about your assertion that rearranging the visual party order has no effect on indexing. Pitbull has an option to arrange party frames by name, and when that's enabled party1 always targets the first character in the list, even if that character isn't the party leader. I'm not sure if this is a standard part of the Blizzard API though, so that may be the only situation that works as such.