I would be tempted to keep things as simple as possible, probably by simply eyeballing what spaces should get X number of modules, and be willing to fudge things a lot so that scores feel right. Fundamentally given how the system is already abstracted in terms of representing the inside of a 3D ship via a 2D view, I don't think that adding too much complexity in the name of fidelity is necessarily a positive here. So long as the end result gets total Science scores that feel sensible, and provides interesting choices for voters, I think that's the main goal.
Also:
A friend shared
this tweet with me today and I thought it was both funny and rather interesting. May go some of the way to explaining why Earth in Star Trek has such an abiding respect and love for the name Enterprise. The link is above but I've also included a screencap below in case it requires a login to view:
Also interesting to note that ramming the enemy when all else fails is apparently a bit of a tradition for ships bearing the name
Enterprise!