Update to this Update:
Yeah... so... I went ahead and, last night, I finished the workaround I was talking about. It actually turned out! I made it fit the plot to have the Ganon battle occur in another room (in the basement, adjacent to where it was going to take place). In the room that I was talking about, with the shutter, I made that door unreachable while, to go through it, you'd have to come around from another way that's accessible after the Ganon battle.
... I'd better shut up, now.

I don't want to spoil it for any potential players reading this.
@judasrising: Thanks for the advice!
... Play it
again???
Awww, but that'll take too long!!! I wanna' release it
now! (/childish rant)
Seriously, though, I hadn't thought of that. I might find other things that I missed. ...
I thought that's what Beta testers were for... but nonetheless it would be a worthwhile endeavor to make sure it's as good as I can get it first.
Especially if I'm the sole tester for version 2.10 (not sure if anyone wants/can do it in that version); it should be near perfect before others check it for compatibility issues/glitches unique to version 2.50.
@Moosh: ... Dang. Maybe I shoulda' waited to implement the workaround until a day after posting the update so I could see your reply!

That's something I didn't know/consider. I'll have to play around with that more and see how it works. It sounds like that would've been a simpler solution!
Of course, I think
one problem I had is that Ganon may not have appeared because I had the player
insta-warp to an identical screen with the Ganon room type. I don't think he appears unless the player walks into the room from the side.
However, that probably only caused Ganon to not appear (also annoying, but not the same issue); that still wouldn't preclude me from trying your suggested solution. Even if Ganon's in a different room, I could still try what you suggested. I haven't yet used the boss room flag for any other enemy room in that level yet (luckily, since I took out the last one with the old Ganon room and didn't change my plans THAT much), so I could try making a secret appear somewhere else after he's defeated and see how it works.
Thanks!

A very intriguing idea. I think that is exactly the solution I was looking for. I look forward to seeing if it works!
@EddytheOliveira:

(See my own childish rant in my comments to judasrising.) As long as you indicate you aren't serious, I take it as a joke. No problems! (A bit of advice, though, to make your jokes sound less offensive and more like a joke, try
not using all caps. If you aren't "yelling", less people get offended.

{And no, I'm not offended.})
Yeah, I think at least
part of my plan had to be done, the part about moving Ganon to an adjacent room. Luckily, my workaround didn't take long to implement.

Now I just gotta' get to work playtesting again.