I think I've got a solution for you. It is something I've done before, and I think it addresses the issue.

2 map exports from FT.

The first one is your normal terrain, but with shading turned off. No shadows, just the plain colors.
The second one is just the shadows. Go to your Altitude color menu and change it to do 1 color each for sea and land, and do them both as White. Then turn the shading back on and export the map with the same size settings.

Take both images into Photoshop, layer the shadows over the terrain and set it to Multiply. You can change the opacity of it to suit your needs, paint under it, over it, mask it, whatever.