To think of it, why do we still have 2 different upgrade mechanics to begin with?
Factories and cybran shields use mechanic that was invented in FAF that takes total cost of next stage and applies a discount according to current cost of building. This allowed to get rid of such things as cheap rebuild and veterancy not taking full unit cost into account. For example currently Cybran ED5 shield costs 4.26k mass, but each stage costs 160m->300(460-160)m->800(1260-460)->1200(2460-1260)m->1000(4260-1260m). You dont build new structure from scratch, you just add more parts to existing structure so it is logical it costs less to upgrade rather than building new.
Other factions' shields and mexes use old upgrade mechanic that uses full price of unit every time you start an upgrade. This ofc allows you to exploit self-destruction of t2 mex to reclaim 800 mass and build t3 mex. With new upgrade mechanic upgrade would cost 4600 mass and building from scratch would cost 4600+900+36=5536, making self-destruct almost never efficient.
I remember talking about it to JaggedAppliance years ago. He said its weird to have two different mechanics. Years passed, nothing changed.
I guess its easier to ignore the problem than solving it.