If you overwrite your override_tiles table declaration with

override_tiles = table.reverse({
--Vanilla tiles
"out-of-map", "grass", "grass-medium", "grass-dry", "dirt", "dirt-dark", "sand", "sand-dark", "water", "deepwater", "water-green", "deepwater-green",

--Alien Biomes Tiles
"grass-red", "grass-orange", "grass-yellow", "grass-yellow-fade", "grass-purple-fade", "grass-purple", "dirt-red-dark", "dirt-brown-dark", "grass-blue-fade", "grass-blue", "dirt-red", "dirt-brown", "dirt-tan-dark", "dirt-dull-dark", "dirt-grey-dark", "red-desert-dark", "red-desert", "dirt-tan", "dirt-dull", "dirt-grey", "sand-red-dark", "sand-orange-dark", "sand-gold-dark", "sand-dull-dark", "sand-grey-dark", "sand-red", "sand-orange", "sand-gold", "sand-dull", "sand-grey", "snow", "volcanic-cool", "volcanic-medium", "volcanic-hot",

--Append Other mod tiles here

}),

it will work to generate proper underground surfaces with and without the alien biomes mod.

Basically, I just added the tiles that alien biomes added to your table, so that it can check and overwrite them properly.