You have to be very careful on the ordering of colony modules in the components file. SE4 assigns the first tech req area of the first colony module it finds that can colonize the HW type (assuming it is not a racial tech, in which case I believe it goes to the second tech req area). Universal colony modules need to go at the end, after ALL normal colony modules.
Additionally, universal colony modules need to have both more total tech req levels AND more tech req areas than the standard type, so that the AI will see them as more advanced.
Adding redundant tech reqs (such as 5 entries of Rock Colonization) works well to fool the AI.
See Adamant Mod for an example (it also has Ekolis' Colony Tech Mod or whatever it was called incorporated):
Adamant Mod Data Files - 506.90 Kb