The arcpy.ListRasters() function will give you a list with the filenames of all the rasters in a given workspace. This way, you can specify the first GDB as your workspace and get a list of all the rasters in it. Then, you can repeat this process for the second GDB.
CVR = r"C:\Aquifer_recalc\Aquifer_recalc_NA\Treecover_NA\Treecover_Inputs.gdb"
LSS = r"C:\...
As usual, it was a simple thing that was missed. I had neglected to set the output coordinate system and apply a transformation. I added these lines at the beginning:
env.outputCoordinateSystem = arcpy.SpatialReference("NAD 1983 UTM Zone 13N")
env.geographicTransformations = "WGS_1984_(ITRF00)_To_NAD_1983"
The rasters then rendered properly.
I wondered if your code was only applying itself to the first instance, as the indentation isn't correct for a for loop.
for index in index_list:
# set extent
env.extent = index
env.snapRaster = index
env.cellSize = index
This might make the code apply to all the indexes in your index_list.