All the Napoleans are freighters that are exactly identical, only difference is the drives, they are exact same size, only difference is power output. It will happily build some of thé much less powered ones, but not the ones close to power and certainly now any more powerful.
Why oh why can I put on much smegtier engines but not close to identical ones? Who knowes? There is no rhyme or reason. I mean, I could get bigger or smaller engines, even different tech, but they are exact same size and technology. Hell, even an argument could be made that large engines would need larger tubes to feed them sorium. But why the close to identical engines?
It would be much better if I could build ship hulls and then fit them with tech that fits into the appropriate hull points that I have designed
This depends on how you see things... from a role playing perspective it might not be so hard to rationalise.
The reason for this technically is that the engine become more expensive and complex as you get new technology and the rest of the ship remain the same from a technological perspective. This means that the engine are not a huge part of the cost and development effort at lower technologies which they are at a higher technology. Thus it is easy to remove lower tech and replace them with more advanced. It is far more complex to replace a high tech engine with an even more complex high tech engine thus it require a change to the yards.
It actually makes sense if you think about it.
You look at the change in cost from one part to another in comparison to the total cost of the ship. In a low tech ship the engine is relatively simple and a lower cost of the the ship and much easier to remove and replace. If you have more advanced engines then the percentage of change in cost and effort is just so much bigger.
This is why you want to think about upgrade possibilities of ships in general. You actually can gain allot of benefit by designing ships that are easier to upgrade, it can save you both time and resources.
You have to look at things a bit more realistic... if you have an engine who is more integrated into the entire ships systems it is harder and more difficult to remove. This is simulated by the fact that the mechanic look at the total cost of removing and adding something based in the total cost of the ship. So... a ship with just one purpose will be more and more expensive to upgrade rather than a ship that can do many things and who can upgrade in many more incremental stages.