General use IO pins can not be used for encoder feedback as they are read at 1000 times per second, that is to slow for anything usable, but they are very usable for MPG encoders and if set to Mode 1 or 2, both Mesa 7i76 and 7i70 will have inputs especially for two on each board of those MPG encoders.
There are other Mesa boards that can easily add that capability of reading high speed encoders, i think one of them is 7i85 but i am not sure, although in your case you already have both ports on 6i25 occupied.
I better leave this to PCW to answer as he is the Grand Master at Mesa.