Only D1 games are worked into most rankings including RPI, but if it's on your record that you lost to a non-D1 school, you're not doing yourself any favors come decision time when really any of those rankings matter anyway.
2 side notes:
1) Honestly rankings for SFA only matter on the seed line 12-16 for the NCAA tournament, not for making the tournament. At least in the tough WAC, we're going to have to win a ton of tough conference games to get a good WACVegas seed to win and make the NCAA's. No WAC champ is getting less than a 14 seed this year period. (So don't really worry about rankings this year)
2) If you lost an "exhibition" game to a scrub school, people would still know, and it would affect decision making in March even if it's not supposed to. But, the likelihood of losing one of those matches and being the NCAA qualifier is something that usually can only happen in the Southland.