The workflow chain would look something like this:
1.)
Conceptualization/Mechanical-Theory - Self explanatory. How would it look and how would it behave etc. Basic layout and art direction. (No tools needed yet.)
2.)
Graybox Interior Map Model - This would include the bit of the map that the units actually walk on etc. (Any sculpting program would work here. Even a terrain editor would work, provided you can export the mesh.)
A. Note that if your map is irregular in design when it comes to the actual environment (like a map made entirely out of metal with mechanical parts everywhere and no real hill/mountain structure) you could simply combine this step with "3)" and separate the "map" mesh with the "decor" mesh.
3.)
Graybox Exterior Mesh Model - This would be everything outside of the walkable map on to the horizon. This would also be the "edge" structure of the map. (Cliffs, walls, ravines, etc.) It's nice to have an obvious edge to the playable map as it let's players know where their bounds are exactly without having some ugly fog/mask effects. (Any modeling software. Max, maya, mudbox, softimage, etc. Depending on the art style for the environment, you may or may not need a sculpting program.)
A. Note that if your map is something like an island, or on the coast, your outside mesh doesn't need to go on to the horizon as the water does that for you.
B. The "edge" structures can intrude on the "map" boundaries itself, as you can just block off those areas in the pathing map.
4.)
Planar wrap the Interior Map Mesh - For the obvious reasons. Don't paint the texture yet though. Just wrap it.
5.)
Wrap the Exterior Mesh Model - The way you wrap this depends on what is in the model itself. If it's it a hill/mountain esque mesh then planar is probably the way to go. If it's more complex, then piece-by-piece mapping is probably needed.
6.)
Temporarily Combine the Interior and Exterior for the Texture - For this you'd combine both the map mesh and the outside mesh for texturing. Don't paint using a 2d paint program like photoshop. That would be silly. Use a 3d sculpting program that supports painting. (Mudbox, zbrush, etc)
A. Make sure the texture for the exterior mesh is somewhat scaled correctly to the texture of the interior mesh. This will vary depending on the complexity of the outside mesh.
7.)
Paint Pathing/Feature/etc maps onto the UVW of the Interior Map Mesh - Using a 2d painter program is preferred here, I guess.
8.)
Separate the Exterior and the Interior Mesh - Prep for baking and exporting.
9.)
Bake from the Interior Map Mesh - Now bake the interior mesh for the heightmap. (Use whatever modeling program you are using to achieve this. Either do a distance bake or just wrap it cylindrically with a grayscale and render it orthographically from the top.)
10.)
Export the Exterior Mesh - Prep your exterior mesh and texture for usage. Use it as a feature, and place it at the exact center of the feature map.
A. Make sure to keep everything scaled correctly. It would be undesirable to have the interior and the exterior not correspond.
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It sounds a bit overkill sure, but that's because there is no editor that can do these basic operations for you. You'd have to do them manually.
The reason this would be so much better, is that it brings artistry back into the art itself. I think a big problem with the way maps are being made here, is that it's so code driven that there is no real art aspect to them. Now, this is not to say good jobs haven't been done. No disrespect meant there ofc, as there have been numerous amazing maps made. But this would just be a more streamlined and logical approach to it. Art should be made artfully.
As for how other games do it, to my knowledge, it's mostly done the way I mentioned above. The difference is that there is an editor that does a lot of the menial operations for the artist. (Things like generating the heightmap for the playable area and separating the two mesh structures.)
LOT'S OF TEXT.
Here's the condensed version.
Since the outside map isn't interacting with the units, it can just be a big feature.
Any part of the feature that is inside the map bounds can be blocked using the pathing map.