I have made a script that tells how many rooms, chests, levers, big chests... have been completed. (please no comment on how badly it's written, I didn't really care)
http://pastebin.com/phSLwKVL
Now I need to find out which of them give how much %.
I make rough estimates at line 511. Tutorial content may not even count. So I'm going to cheat myself out of the tutorial by using address
02020FE6 which stores the room that I'm brought to after I die.
(If you cheat yourself into Darkmind intermission rooms, the big mirror there will be incomplete and not let you move on)
(The beta room and possibly the arena-only rooms (I didnt check) have own flags but the game gives 100% even if you didn't visit those, of course)
...
0065 = Rainbow Road 1
0066 = Radish Ruins 26
0067 = Rainbow Road 5
0068 = Rainbow Road 4
006A = Rainbow Road 2
006B = Rainbow Road 6
...
0088 = Rainbow Road 16
...
0144 = Mustard Mountain 12 (Kracko)
...
0212 = Cabbage Cavern 2
...
0323 = Tutorial 1
...
0337 = Olive Ocean 10
...
0390 = vs DarkMind2
0391 = DarkMind Intermission room (Water)
0392 = vs DarkMind3
0393 = Darkmind Intermission room (Ice)
0394 = vs DarkMind4
0396 = vs DarkMind5
0397 = vs DarkMind6
...
03B6 = Ability room (Arena)
03B7 = Intermission (Arena)
...
03BD = Arena room (Arena)
...
03C9 = Beta 1
03CA = Ability room
----
8 rooms = 1%
15 rooms = 2%
23 rooms = 3%
therefore 1 room makes up ~2/15 %. (34/256?)
22 rooms + 2 chest* = 2%
22 rooms + 3 chest* = 2%
*1up, meat, 1up
therefore 1 chest makes up 1/31 ~ 1/45 %. (8/256?)
The tutorial rooms, the tutorial chest, the hub room, the ability room and arena-only rooms do not count.
The Dark Metaknight room, all Darkmind battle rooms and the intermission rooms do count.