That's right. The wreck value is based on the unit cost, and upgrades cost the full new unit cost, not just the difference between the new and old unit. It is a little counter-intuitive.
Strange to me too. Worse is when you try to build over the wreckage of destroyed hives/kennels and the wreck and engi station you tried to build instantly disappears, instead of rebuilding at 50% or reclaiming first.
Guess trying to make that t3 engi station wreck into a t2 engi station is too OP.
It's just a quirk in the game that wasn't thought about. When you upgrade your old unit disappears and a new unit, who looks exactly like your old one appears and starts upgrading into what you wanted. rebuild and wrecks weren't even looked at.