Bug answers:
1. Sounds like a ZC bug with the F1 feature which I rarely ever used, if ever... but I look at those screens.
2. Yes, the "invisible" checkbox means only the player, your weapons are always visible. I don't think that I will go on an put everything on layer 3 and above to prevent this.
3. You mean the first Spellcaster's Choice room and to the right of it? I can change that around...
4. Yes, I found that funny glitch, too. I kept pressing onto Myra and was funny when I walked over her. I can't avoid this happening, but it one of the earlier updates, I wrapped the screen around with solid invisible combos, so at least you can't jump off the screen anymore with this fun glitch.
About dragon heads... WHAT?! I NEVER knew you could shoot dragon heads... And as far as I know, ZC is the exact copy of LoZ, so then you should be able to shoot dragon heads, too... But it's not up for me to decide, you can't change enemy weakness and attributes in 2.10 (only choose from 2 enemy sets, the small and the long). Such thing wouldn't be possible in 2.5, either, since the detached head isn't a separate enemy and also disappears when all heads are cut.
Questions:
1. "Mako" is the processed form of the Lifestream which is the blood of Earth in Final Fantasy VII. Materie is the crystallized form of Mako energy and Lifestream, used to cast magic and gain special abilities (best equipment system every). You know, BB is the sequel of all videgames, movies, comics, etc., so don't be surprised when you see lots of relevances to other games. The Goron King in Glacier grotto was infused with too much Mako energy, so he became a monster (like Hojo in Final Fantasy VII). Myra is called "Mako girl" because the Goron king realizes that she is full of Mako, too. If the four endings you saw didn't make it obvious, find the 5th ending.
2. This is just for drama. The whole world changed, many things got destroyed, even part of Mt.Death collapsed, but that small flower there survived everything without a scratch.
3. In the potion house? Potions. Use the empty bottle on the screen to make her start selling the potions. Just like in LoZ. You know, I made BB while thinking that all players will know all Zelda games and also such big games like Final Fantasy, Mega Man, Ultima, etc.
4. You aren't supposed to get back to LW, nor to have ocarina at that time, so there are no ocarina triggers in LW. I put them there only for realism. Just because the player doesn't have ocarina, it doesn't mean all people must forget about music, the world doesn't revolve around the player. That "girl" (in fact a male Skullkid, play OoT and MM to find out about him) originally said "Music?" only to have a reference for OoT, but now it has an extra meaning. It is a clue for that you need to use ocarina at the exact same screen in IW (Skull Woods north).
5. I guess it's the "Mysterious Item/Unknown Item". It's in the last dungeon, just near where you get the clue on how to find Secret DX ending. It makes you invincible for everything but enemies and fireballs, so it's not good to get it for first playthrough, makes the last fights boring.
6. That's not woman, that's little girl. And you can't get in the building. Since Kokiri Downtown already had enough interiors (shops,walk-through screens, minigame, slash learning, story related, etc... far enough), I decided I don't take time for putting something even there. Otherwise according to original plan, when you slash the girl's clothes, somebody from the building opens the door, comes out and you can go in.