I believe that both of these are true and that when put together, makes and even bigger difference to why they look better top down. If you look at a coral in your tank at a higher angle (but not top down) it will look different than if you looked at it level straight on, and that will look different than if you look up at it from an angle below (crouching below eye level of the coral).
Interesting topic to bring up John.

Take a look at Sanjay's lighting pages. Several of the DE bulbs give PPFD numbers with glass, and without glass. There is very little difference. The glass does not block very much of the light.

So, why then do clams also look different through the glass then they do top down?.....I have one crocea that looks purple through the glass but is green top down.

Iridophores have groups of cells that contain reflective platelets which act as light intensifiers. Depending on the orientation of the platelets, relative to incoming light, They can defect the light away or towards the clams eyes. That is also how the clam can react to a shadow of a hand passing over,or the difference of appearance form viewing at different angles.