FlyingBlue definitely does this. I recently booked 2x one way tickets on the exact same J/D1 flights RDU - ATL - LHR (all DL metal) with 1 ticket booked through DL and the other through FB (booked at the exact same time to make sure we both got on the flight).

The one booked with DL miles was $5.60 while the one booked with FB miles was ~$23 (as listed above though the charge was in Euros). Didn't bother pursuing but it definitely happens - not sure what there is to do about it. I think they probably know it happens but figure most people are like me and are pleased with getting a TATL D1/J flight for ~$23 + miles that they don't both pursuing the overcharging on taxes which they likely pocket directly.