This is true and a bit unfortunate. Especially changing the order or adding new options in later after an initial authoring. It's also a bit weird that when adding new branches they always come 2nd from left. There is some sort of auto ordering there though. Is there a logic that you can pick out between the order in the editor and the client? I think I remember @tnelson hacking around with this to get it right, but if so it didn't sound like a lot of fun to delete and painstakingly re author in a specific order.
I wonder if a downloaded game file would indicate the ordering in a way that you could swap indices and re upload? I'll mess around with this a bit when I can.