@cyborg16 Besides color highlighting tech 3 / tech 2 engineers we can also adjust their strategic icon sorting order. That way, they always get rendered on top of tech 1 engineers.
It appears this should already be the case (as the value of t3 engineers is 85 and those of t1 is 105) but it doesn't always happen.
Value of 40
Value of 85
I think adjusting these values accordingly may help fix at least the engineer situation you described.