In the 6 conference, BCS world that was, RPI worked a bit better, because almost everyone good was in the BCS conferences, the A10 , MW and CUSA of the day got a little "push" because they played more BCS teams than their peers, and you were comparing relative "equals". An individual team could "game" the RPI, but only within limits. Play non-BCS teams that dominate their conference and play poor BCS teams from other conferences. The tricks were well known. And the non-BCS teams suffered a bit for it, except for the noted conferences.
Now, you have BCS teams, so called, NOT in the P5 conferences. Teams in the American and BE are disadvantaged because of the weakness of the bottom half teams (this affects the A10 as well, the MW and CUSA faded due to realignment). Meanwhile, the P5 RPI are inflated for the reasons you mention.
By the way, teams play lousy OOC conference schedules for a lot of reasons - for example, sometimes your OOC opponents are not as good as expected (St. Joseph's for RU, Temple was a question mark for a while), other times you just need wins, baby. See Butts, Niya, probably not surviving this season. Teams play OOC mostly at home because it is financially to their benefit. If you were to list RU's OOC schedules for the last 10 years, home / away and "where away" - you will quickly see that finance went into it as well. And RU can't be the only school.