Before 1.44 you could have multiple squad in 1 squad.xml by wrapping all squads in a root node. After extra checks this is not possible anymore without errors in RPT and an XML file is invalid if it has more than 1 root element.
I haven't tested if it works in-game, but the XML is invalid and it shouldn't be.
Allowing us to add a wrapping element (can be specified by one name so you can still validate XMLs on your side) would be great.