I gave this some thought long time ago, your idea Jip makes perfect sense. Mass is mass and should have HP that is consistent.
maudlin27 makes good points about the strategic nature of play, you would get players who just see the game as an eco race and would consider mass in the base better invested than sent out onto the field, and if you can always rebuild T3 arties or game enders at half cost or reclaim the wreck to make a new one then why would anyone risk donating mass into a heavily shielded base.
CasterNumeroUno also makes good points too. If we consider that there are processes in manufacturing where you take materials and convert them into other products, often times it is uneconomic to recycle them into their base components. Using higher tech units with likely highly processed components we may have such a case where the amount that is recoverable is much less than the 81% standardized amount in the game. Unfortunately we only have mass and energy, but nothing in between such as tech'ed up mass. One would have to probably go ahead and make a judgment on whether to decrease the reclaimable mass amount through the tech levels to leave the reclaim with a consistent HP amount per reusable mass unit to get a better result (a lot of work based on personal judgement which will be cause for more infighting and hate :p).
The source of the current issue lies in the fact that the mass cost of a unit does not translate directly on a fixed ratio into the HP of the same unit. This is why a one size fits all approach does not work well across the spectrum of units.
To get a better outcome for the Fatboy, the easiest short term solution would be to increase mass and energy cost by 25% and raise HP from 12,500 to 40,000, because it is a big tank and doesn't reflect that in its stats.
Also, you could always go through every wreckage stat of problematic units like radars, Fatboys, etc and change HealthMult = 0.9 to HealthMult=10 (radar) or 3(Fatboy) or to any other desired number that leave more HP on the wreck though for units where the logic of a huge clump of mass disappearing is very problematic.
Have you thought about how much HP 1 mass unit should have in your standardized solution?