Yes, having the player choose to enter the level is more of a debugging feature than anything, and will probably be removed from future versions. However I have in the latest version included a pause menu (only on the overworld), should the player find themselves needing to take a break mid-session.
Mini-games are chosen randomly from all possible games at the start of each difficulty. So you can indeed play the same game twice, just on different difficulties, in one run.
We are also in the process of spicing up the final boss so that the platforming section naturally progresses to a more interesting final conclusion. :)