When manually editing a DMM file, you can modify a type like so:
"a" = (/turf{z=16},/area)
And the z value will stick around in the DMM file.
When you run the world, though, it won't actually change the location of the tile itself, and the tile's z value will of course, be wherever it's actually located. The world's maxz value will also be whatever it should be based on the size of the DMM file.
I actually found this useful for embedding excess metadata into a DMM file that allows me to do some interesting things when edited in an external editor...