I don't know how to do something, I'm not familiar with it. But as an idea, I can suggest creating an additional .h5u file in your campaign pack, and adding only DefaultStats to this file. Then, you can create 2 simple batch files to enable and disable the file, and in the mod description, indicate that this file should be enabled during the original game + Lords of the North (and it will not be possible to raise alt upgrades), and during the game in Tribes of the East, disable this .h5u file through a batch file, and then you can raise alt upgrades again. But this is just a random ideaon practice, this will be a hassle for many.
An Archer is upgraded to a Skeleton Archer - this is recorded in DefaultStats, but the ability to change the upgrade (most likely) comes from the ability to upgrade the basic skeleton to version 2
on practice, this will be a hassle for many.