I think I got the secret ability (the one from the Gem Scratching Post?) I got it before fighting the final boss. I actually think I collected everything except the items behind the Sunset Gates before defeating the final boss. The secret behind the 99 door is the very last thing I collected before going home. So I was able to get all the other optional items without using it :)
I did notice when I got to the area behind the switch block in the Neon Lair that I could have actually gone there earlier, but I don't think I realized how open that part of the game is. I went to that area to get my sixth cube. I actually really liked the moment when I got five cubes and then realized I didn't know where to go next because there is no five-cube door. I had to think about where I hadn't explored yet in the world. But I guess some players wouldn't like not knowing where to go and would get stuck.
Thank you for the wonderful game!