For whatever reason all the coastline polygons for my imported model (shown in the first attachment) are very darkly lit at night and too bright at day. The second attachment shows an earlier version of the model with other lighting weirdness that I've fixed, but doesnt have the weird lighting. Other than combining a few sections I havent touched the coastline.
So I realized after posting this that the 4th gen games use dynamic lighting on their maps to give the faces of mountains a shaded look that changes throughout the day. Game Freak is using a setting on the beach polygons on their maps that makes them ignore this. I was confused by why it seemingly didnt appear on the older version of the map but it actually does. Looking at the model of the older version it looks weirdly smooth compared to the current model, so I must've accidently ran a smoothing command on before I exported it to .ima format. I don't quite know how this didnt push the model beyond the polygon limit unless it managed to without doing that.
I was looking around and testing the NITRO settings in 3ds max but I was confused when no setting seemed to cause the desired effect. Looking through the SDK from DSHack, it turns out there's a tool, 3DMaterialEditor, to edit the settings of the exported .ima before converting it to nsbmd! I haven't tested it yet but I thought it'd be of interest since I don't believe I've seen anyone else talk about it. Hopefully I'll be able to figure out the correct settings.
You'll not find any answer in the materials - because it is in the vertex normals! I still need more research, but I've managed to delete completely the weird shadows of my polygons by setting the same vertex normals' value in the whole IMD file.