I asked myself the same question, and it pertains to big changes in the game field itself. Consider the old game Rayman: The Great Escape. Yes, it is kinda old, but it is a perfect example for my point here: In the game, you enter levels or scenes where you can control Rayman in mechanics and points of view that vary. One level requires Rayman to ride a rocket away from the camera (we see his back) along the Z plane of dimensions, while another requires Rayman to run from a boss the opposite way (towards the camera, we see his face) along the z-plane. Clearly there is not currently a z-plane in Buildbox, and that is not my point. My point is that the are level-specific forms of gameplay itself, and Rayman The Great Escape has examples of that. Doing this in Buildbox would require a kind of ability for enabling big changes to the game field (where you edit the game play and where the gameplay takes place) itself in a way that varies by level. For now, it seems that the main things we can do is use strategically made "gameplay actions" features to make changes in the gameplay in the gamefield. I am not sure that these action features would enable the types of level-specific forms of play I mentioned. I guess it depends on the shift in gameplay and the auto-scroll properties of the game.
We messed with this idea in an update to Revolution. (But as we could not separate the two mode scores in Game Center we dropped the idea). But basically we had normal mode - just hit play. Then had a nightmare mode set up via a button (which was actually a next check point to access levels set to a really high number you would be unlikely to access via normal mode). Nightmare more hade a changed up dark colour scheme and was really hard. So that's an option to think about if you can forego the points thing.
You definitely could create game modes but it would be with out a break in game play. Of course this would be due to using gameplay actions as stated above. I feel like we are all in for a treat with that we will be able to do with BB 2.0.