You are looking at all or nothing,
1 not all programs (milkshape) can work with LOD files.
2 if it LOD works, if they use outside peices the ships will be seen only as peices inside the game at a distance
3 not sure if a partial model is exportable
4 LODs require textures, normally at reduced size and resolution to be effective, this greatly increases the file size for each part
So well it is a nice idea it is not practical and would add needless complexity to your project, which is already complex. Best bet, if it can be done, templates work for those that will go the extra mile, most will not as it adds extra work and will not be useful moving ships from one game to the next.
So if it were me I would worry about the about the parts and making them interchangable. Once that is finished then look at templates.