Took a little research (had to google what a Phong ). To begin with, I’d just like to point out that I’m round the hobbyist/amateur level when it comes round to 3D art. When there’s a particular effect or process that I’m trying to do, I look for tutorials and whatnot on the net to learn at the time. My art training ended at school, I’m afraid 
Appreciate the googling
1) I kind of suspect Nexus (or its converter) doesn’t. On occasion I’ve had a model with an odd shaped poly that looked good in LW but once converted, that odd section was changed. Personally, I prefer to triangulate the polys myself as (especially on smoothed out sections) as it can reduce or remove artefacts.
As for Maya, I did a quick google search… I think what you’re looking for is under Meshes > Triangulate.
Ah makes sense. Yes I found it in Maya
Having triangulations in the mesh will of course increase the poly count, but when the original ship only has 3k poly's, that still gives me a ton of room to play with.
2) The majority of the model goes in one layer, while moving parts need to go in separate layers. So each dock door (because they move individually) would require its own layer, whereas something like a radar dish or a rotating ring, that entire section would go in a layer of its own as the polys required to make it need to move together.
The best way to figure out which sections need their own layers would be to use Nexus’s model viewer and watch the animations on the original models (1 - 0 starts them, crtl + 1 - 0 stops them).
Didn't even realize that there was a Nexus model viewer and that you could view the animations in it. That's helpful!
3) If I understand this one correctly, how much a section shines is based on the spec map that gets loaded into the colour maps alpha channel. Things like reflection or transparency also require some settings in LW so that the converter understands what that section is supposed to look like. But for the most part, I try to achieve the visual effects in photoshop as much as possible. Descriptions of the various texture maps and how to use them start on page 14 of the modding manual.
Right that's basically what I was saying. In Maya, a phong is a type of material, kind of a plasticy look. In the full version of Maya, there is also a blinn, which is used for metal type surfaces, and lambert for non reflective surfaces, among others that I never used. I do my texturing in a combination of Photoshop,Bitmap2Material, Substance Painter, and Substance Designer.
What got me wondering was if I assign a phong, a blinn, or a lambert to a model prior to exporting the model into say, Substance Designer, for working on the texture, will it impact the actual final look versus I had assigned a blinn instead (if that was even possible since I'm using the Indie version of Maya and thus can only use phongs). It's probably an answer you can't answer. My suspicion is that no, it doesn't matter, since the texture maps are the driving force in how it ultimately looks. But I'm not 100% certain about it.
My Update:Started working on it today. I'm about to hit the sack, but didn't make much progress. I had a decent chunk done, then it occurred to me that maybe all the various meshes that were kept separate was done intentionally for either animation, or being able to target certain parts of the ship, or something. Decided to instead just use the existing mesh and slowly work my way around and use them as a reference and improve on them in whatever way I can.
Now that I know that a Nexus model viewer exists, I'll have to locate it (I assume its either a mod tool on this website, or in the install folder) and give it a whirl. I think once I have a better understanding of how the ship operates it'll be a lot easier for me going forward.
Long term I'll have to read more up on how to do the assign engine points, and gun turret stuff, and whatever else I need to do. Also wonder how the animations will work, does somebody have to re-do the animations for various things (if required)?
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