Sorry If I try to respond, but if I've undestood correctly you want to play, for example, today the original playthough and tomorrow the variant without worring about overwriting saveslots of the original playthough with the savings of the variant and viceversa.
I don't know if this could work, but you can copy the entire folder LustfulDesires-0.43.2-pc and renominate one LustfulDesires-0.43.2-pc-original and the other LustfulDesires-0.43.2-pc-variant. In this way instead of being careful with the saves, you generate two different sets of savings that don't interfere with each other.
Note that in this way you can't make different choices with Nameless and you're forced to repeate them in both playthough.