I believe there is a need for an update on this one.
First of all: hitbox works. Though it wasn't easy and known methods to me didn't produce the result I needed so I had to go hard path through experimenting, trial and error.
The result however is not ideal, and understand that collisions between two complex meshes are never ideal, this is due to the way the game works and optimizations of the physics engine. Let's put this way: this isn't Havok (a well-known physics engine for games for those who don't know, I used to work with it before), it isn't that good and has a huge pile of limitations, bugs and so forth.
The good part of it is that it works, damage detected, and where gap are you can shoot through.
Shrink-wrap shield was replaced with proper shield bubble as it should technically be on ANY ship that can have shield. Currently I'm not going into details and explanation of how these things work, that's a topic for an article I might be writing soon, but basically what it means for you that the ship is the shield is easier to hit, while hull hitbox follows the shapes of the model almost exactly.
Understand another thing here, the model itself is complex for physics engine, it works but a complex hitbox such as this one doesn't go well against another complex hitbox, and this is much true to any ship larger than fighter. Stations however work fine and I "hugged" Newark to death of my ship without being able to slip into it. Same tests were performed at West Point station.
Conclusion. We have a first ship here in discovery with its own custom hitbox and it works.
I've added turrets, proper arcs, some other nice stuff, the only thing remains to do is to put nice blinking lights to make it a real xmas tree now.
Don't be so happy about it, the solution through which I found it getting to work is pretty rough and ugly, I'd rather do it proper way, but there are technical issues right. So, for now I'll stick with this one until a better method becomes possible (which will require tweaking exporters code, have a few ideas but once again - no guarantees yet, that's gonna take some time).
Anyhow, I'll need volunteers to test the hitbox. Although my tests were fairly successful as to the result I was looking to archive I still need few people try it as well. This is only for those who know how to put ships into the game (shiparch, goods, market and engine editing), I'm not providing guides for people new to game modding. If you wish to participate in test - PM me. In the return I'll need reports of crash collision tests, and so on.