You can display each type of collision box in a different color. Currently, you don't get to pick your colors though, since we just stole the code from our hitbox debugging mode.
I don't think you can fall through a hole smaller than your collision box anyway, but there are bugs related to standing on the "space" between blocks in a stack. If you get good at it, you can climb vertical walls, or jump off of the tops of doors. We've taken steps to insure that it can't happen if you build the levels properly, but more aids to help with proper level building should come in the future.
There's still a laundry list of kinds of "doing" we need to get figured out before we even start developing a properly inclusive way to un-do, but rest assured that it's a significant priority for me as well. Since constructing a script to recreate the level in game space is the main function of the files this program will create, storing a list of changes to be made to the design space should be able to use the same notation in most cases. Once the notation is worked out, it just becomes a matter of storing that data and applying it consistently. (That's more work than it sound like, but it isn't infeasible.)
What else do you need? We deliver in 70 years or less.