There are two puzzle rooms in the Black Tower. The southern room is the one with the glitch. I don't think it affected the story or gameplay in any way. Maybe there was a nice prize if solved, but it certainly wasn't anything vital as is the case with the north room. Before I found the miniguide, there were areas I crudely mapped out by hand (land, air, sea) and was thrilled to see those maps in the mini-guide. The only other place I felt the need to fully map was the forest temple in the Depths. All that teleporting around. :) That would be a nice addition.
It's the chemist recipe I seem to have missed. I'll be sure to find it on my next go-around.