Clearly a lot of the Vette's extra mass must be coming from what's essentially built-in shield boosters and engine turbo chargers.
I like your answer in that way , it appeals to my logical sense. There are a lot of things in Elite we accept on the face of it (FTL, Flight model and so forth) and that is all fine and dandy, we have to , else no game.
But doing the Ship and outfitting juggle is a bit different, when we build ships and equip them with standard modules, we expect these modules to have the same characteristics, ie a power plant delivers 30 MW of energy and weighs 60 T. Period. It should logically do that in all ships where it can be fitted. Logically and appealing to common sense. I'll buy that as an Engineer myself.
Where things starts to muddy, is when as my example illustrated you have to accept an behaviour of the module that defies logical thinking and common sense. (I am not talking Modding here).
In my example Both the Thruster and Shield Generator behaves in a radical different way, for no apparent reason. (Cmdr's StiTch and Morbad gave some "reasonable" explanations to these factual behaviours, game wise at least). But as an Engineer I find it difficult to accept an incidence that defies what my Calculator (HP 48 GX) tells me is the truth.
This would not worry me, if the whole putting on modules was handled in a way like the RNG Engineers do stuff, then it would be believeable, but as it is FD have tried to make the module fitting "Logical", ie take the same ship, grade up or down the module and the result is logical. Fair enough. But put it on another ship, it might as well be a completely different module :S .
Cmdr bubbabenali points to the "discrepansies" in armour, well that is not so hard to swallow, different materials used in manufacture so forth... (Unless you apply the fact that, the ship built explicitly for a military purpose has got a weaker armor !?! Logic defying

)
Well it puzzzles me and I should let it go, and play instead, but I am having a hard time doing that

I think that the Cmdr's working on mapping module behaviour, strengths, benefits and characteristics are doing a tremendous job, I wonder how they deal wit this...
Handwavium, Unobtainium, Boosterium...?
TL.DR I have acceptance problems.
Cheers Cmdr's