So the sim is not coding these players as 2-way players, even though they were used in that way---as far as I can tell.
The case of Buffinton is extremely strange, since he did have 17 decisions in 150 or so IP, in 1886, but is not coded as a P for that year.
If you just search Buffinton as a position player, nothing at all comes up, because the default search is for 20 games at any position; he is coded at playing less than 20 games at any position (1B and OF). He must have been used primarily in a PH role.
Guy Hecker is a different case, web sources stating that he was widely known as a pitcher and as a hitter, from the git-go. And then he did turn into a position player. I have no idea what the sim is doing with him.
All this being said, I believe we now understand each other and we agree. It would not be allowed for you to draft two Charlie Buffinton's, because they are from two different years, and you could only choose one year of him in any case. So obviously you have to choose one year or the other.
The only problem would be if there are players coded both as P and as position players for the same year. Are there any of those?