To clarify Grymme's amswer:
ORIGINAL: Lava
If you graphically mod the terrain tiles, to play the game you will have to substitute graphics folders/images or have another install of the game dedicated to the new graphics... correct? Otherwise they will overwrite the original graphics.. I believe.
Not correct. To create custom graphics you create a new folder and in the editor select the graphics you want. Then include the custom graphics in the scenario zip you submit to the Scenariobank.
ORIGINAL: Lava
There doesn't appear to be an alternative graphics file type system (think TOAW). Any plans to include something like this in the future?
According to above, it is already included and extremely flexible once you figure out the scaling etc.