I was looking at this, and the system could be useful for my project. The only concern is most
of the swords appear to have mostly the same proportions. Is there a way to preset alignment within your
system on how things should align with unusually different proportions.
Not sure I understand you correctly, can you elaborate? You can scale swords as a whole object without problems, and it’s very easy to define multiple sword types, one for your big heavies and one for your tiny rogues, for example.
My concern is the proportions of individual components such as the hilt, blade, handle.
If components are the same size, does your system know how to align the pieces properly?
I’m still not sure I understand you correctly, so let me explain a bit how our swords are put together. Each component has its mesh pivot placed in such a way that they all fit together - so if you scale them, they all scale from the same origin vector. That means that however you transform a sword, it will always be a single unit that scales as one. (Doing it any other way would just be a complete headache to solve without any gains at all.) Does that answer your question? 
If not I’d be happy to elaborate!
I understand pivot origins, however not all your hilts are same size, not all handles same length, not all blades the same thickness, so how does it ensure that pieces are compatible before it allows the player to try to combine them?