I believe if you have the respawn triggers in the correct order, they will respawn correctly into their slots.
You need to assign a unit slot for each player and then only have that player command a unit in that slot.
Unit slots work like this:
They are the units placed in order on the map.
SCXE farks up unit slots because it reorders the units by going from top left to bottom right going across.
Currently, the only tool to check the unit slots is
SCMToolkit.
You use the number for the cooldown for ALL UNITS.
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Find the post that I posted a program to check unit offset.