It's an amazing concept that perfectly fits your given title. The amount of content created by the layout of rooms, doors and keys is masterful. Given more space, I could see this dungeon support a full campaign. This is the project I most want to see as a full-fletched zine, and I dont even have a Rubik's cube.
The risk I foresee is: You've mentioned that you opted for more small encounters because you'd assume players could get stuck here. If you're correct, you may want to skew the other way; fewer (monster) encounters with more impact. The current setup has the danger of encounters becoming tedious, without much player agency to mitigate them. The fun thing about the monster rooms like the Rat's Nest is that you can avoid them. Random encounters don't have that luxury.
I'm not very familiar with Shadowdark's encounter rules so maybe take this with a grain of salt :)