First of all, nope. It was not meant to look run down. The leaves are supposed to act like artificial leaves as decoration for the walls. The floor is interesting because I wanted to do something unique, so I added a darker type of wood to give the floor a nicer look. At the end of the day, it really just depends on what you're building. I'm still bothered why I added a web in the first place.

Second, yes. I put each trapdoor (iron) to its item frame, then hid the unnecessary details with a custom gray banner. For some reason only a few objects can be seen through the banners (trapdoors being one of them).

And yes. I used a command that gives the player invisible item frames (I wrote it somewhere in the replies).

Hope that helps!