Each franchise has their entire history available, so yes, NL franchises can use pre-1901 seasons.
There are a number of variables I played with in designing this theme: number of leagues, caps, whether/how to allow expansion teams, etc. Depending on how this goes, I may run this in the future with other permutations, but I landed on the current design of the theme after a lot of playing with rosters...I actually think all 6 remaining "original" franchises, and many of the possible expansion permutations, could all be competitive in this theme. (Whereas if we had higher caps - say 140M or higher - I think several franchises would be at a real disadvantage.)