Trees won't grow if there's backwall behind the sapling. Mushrooms (except glowing mushrooms) won't grow underground and usually don't care about backwall.
2) Planter boxes can be set up like platforms, and is more compact. You can plant /anything/ in a planter box not its type, i.e. blinkroot in a fireblossom planterbox. Just remember to leave a tile space between rows so you can actually plant.
3) Underground layer is the absolute nearest you can be to get truffle worms.
4) Only trees require unobstructed sunlight, read above. Not sure if glass wall invalidates this, but I think it might.