if you start your model by importing the old geometry from FFE then you can't go wrong so far as scale goes, as long as you set up your units correctly, but that should only involve multiplying or dividing by a multiple of ten and the correct size should be clear.
The mass is i think fudged, as i said before... specifically on purpose to skew the capabilities of the smaller ships yet keep them large enough to be able to shoot at, or even see.. much smaller and many pirate ships in the original ffe would have never resolved to be any bigger than a pixel due to the low res screen mode.
now if you started changing the mass values, you have a big impact on the balance of the game and combat and how you progress through the game, suddenly starting with much more cargo capacity would make a huge difference.
now lets consider why they
could be reasonable figures:
1, cargo capacity is based on mass, not volume. you might have a lot of something really heavy but thats as much as the ship can lift so your bays might be vast, and largely empty, but another ton of weight and you cant take off.
of course as the game simply models it, the mass of the craft is always observed to be constant despite the amount of equipment or cargo on board... an unloaded craft should leap off the pad with little power, whereas a fully loaded ship would creak and moan, and shudder and shake its way slowly up into orbit at full blast... instead, performance as far as i can tell is exactly the same.
if this were modelled in more detail then it would make a huge difference to being a pirate or a trader, you wouldn't make it off certain worlds with a heavy load, and on some you could overload it.. mass is irrelevant really, it just means you need to expend more energy to move it around and in certain conditions would have to avoid certain gravity wells.
maybe you could only pack on board 30 tons of pillows, or, i dunno, fresh cabbage. something with a fairly low density, but takes up a lot of room alternatively you could probably load up the viper with 400 tons of plutonium or something heavy, right, with a high density, thats the important part. it would fit in the hull but it wouldn't blast off from earth, but you could move it around slowly in space, and grud help you if you crash.
All of this kind of thing is really sketched over in FFE and its prequels, i see no signs that FFED3D are going to address either...
of course i dont really know what 400 tons of plutonium, or 30 tons of pillows really looks like... so my figures there could be off
2, scifimaterials, these can be extremely strong or even very large, but very lightweight.. how do you know the hull isnt mainly a low density foam, several meters thick? it says nowhere in the game about the ships construction or materials, so lets assume its constructed in a way that takes up a lot of room, more so than an airliners hull, but weighs a fraction of a conventional construction.
3, large but lightweight hyperdrives... rather than being a small and dense unit, perhaps these are quite big taking up much of the ship, but dont weigh much, maybe they have a large amount of empty space inside.