I have a heightmap bitmap I generated from NED data that I'm using for a map I'm working on. Inspecting the bitmap file generated from Dmitriy's QGIS style file, it seems accurate, in the sense that a point that my source data says is 57 meters above sea level has the color value (57,2,16), which matches the scheme in the North-East Italy map.
However, when I have Armored Brigade in map editing mode, the terrain type/elevation tooltip says that the lowest point in the 15km square I'm editing is 0 meters, and all other heights are relative to that. Is that something to do with map editing mode, or am I missing a step in the heightmap generation or map creation?
I think the way this works is as the tooltip suggests - the game does not show absolute height, but instead will take the lowest point of the map as 0 regardless of its actual height (colour) as per the height map. I'm not sure exactly why this is done - but I suspect it may be simply to do with how the AI reads the height map.
One thing you can always do is create some labels at key elevation points (e.g. hills) and cross-check their relative heights to see if the height map is accurate or not.
Also, how does the lights.png file work? Is it just an overlay on the map at night, or is there more to it than that?
The short answer is yes! It's a simple overlay. The nice thing about it is that it is a 24-bit PNG, so you can do things like coloured lighting or fog. However, it is not animated, and only appears at night - and, to my knowledge, has no actual effect on anything mechanically.
You can take a look at an example of what can be done with the lightmap file alone with this mod that I've made: https://www.matrixgames.com/forums/tm.asp?m=4670636 (where I added some coloured lights, mist, and light pollution).