i have not played the engi mod yet, but i think it changes a lot of basic gameplay concepts. I suggest another way.
t1 engies could construct t1 units and building at normal rate but on higher tech things slower. It should be most cost effective to use one factory for each tech level assisted only by engis of its level. Of course if you dont want to build lower tech units any more your t1/t2 engis shouldnt be wasted. This concept is very logical. As the game progresses lower tech units/engis should become obsolet but not complete useless. The engine should let you do the translation from t1 to t2 to t3 phase smootly.
Suggestion for changes:
t2 engie build rate * 1.1
t3 engie build rate * 1.25
t1 engi on t2 build rate * 0.75
t1 engi on t3 build rate * 0.5
t1 engi on t4 build rate * 0.25
t2 engi on t3 build rate * 0.75
t2 engi on t4 build rate * 0.5
time to produce t2 engies * 1.5
time to produce t3 engies * 2
t2 factory producing t1 build rate * 0.75 mass waste of 5%
t3 factory producing t1 build rate * 0.5 mass waste of 10%
t3 factory producing t2 build rate * 0.75 mass waste of 5%
t1 factory producing t1 units energy bonus of 20%,
t2 factory producing t2 units energy bonus of 20%
t3 factory producing t3 units energy bonus of 20%
This values are a guess, could be complete wrong but they show the direction. So what do you think?