Scale mount it! Just make it really huge so you can't use it unmounted on ANY ship, then make a series of scale mounts, one for each ship size, where each ship size has a mount that makes it take up a large amount of that particular hull's space. So if you want it to take up 50% of any ship's hull space, and the size in Components.txt is 2500kT, then your scale mounts would be 1% for every 50kT of hull size, so you get a 75kT (3% of 2500kT, since an ES is 150=3*50kT) engine on an Escort, a 200kT engine on a Light Cruiser (8% of 2500kT, since a LC is 400=8*50kT, and similarly for the other ships. Just tweak the numbers for the particular sizes you want - if you want the engines to be more space-efficient on larger ships, but still not a constant size for every hull, you can reduce the mount scales for larger ships.
Now what would we have done had Aaron not put in mounts in the first patch???
