Is there any penalty to using Epochs? Once you get your first mutation point you can just refresh epochs over and over for infinite mutations.

Hi there, yes epochs were an experimental feature. The original intent was for you to populate a new tile every epoch. Unfortunately I've stopped development on Mito, so it is left in a "sandbox" state where you can get as many mutation points as you wish. I encourage you to try playing by the original intent, or to find your own rules that make sense for you!