Although you are right that the numbers dont line up, there is a significant detial you have missed, spesifically the fact that UEF nano regen ocupies the same slot as the engineering upgrades while the seraphim one doesnt. That is part of its 'cost' that you have to later replace it.
The perpose of the UEF nano is to be an early game boost to combat effectiveness, at the expense of being unviable in the late game, because of this it is cheap and does not allow the constructuon of t2 buildings.
The seraphim nano is the exact oposite, its intended as a more late game boost to surviveability without sacrificeing early game capacity.