Any aircraft that loads a flight plan directly from SimBrief is most likely handling this issue - an FMC typically calculates its own climb/descent waypoints.
What we are trying to address is how to (easily) import the same FP into PF3, and unfortunately our current approach, the Flight Plan Filter, doesn't really work for a SimBrief FP.
I am exploring possible solutions, but in the meantime you can either use LNM to 'correct' the waypoint altitudes, or load the NoProc format and adjust them manually. Unfortunately, although it's clearly a bug, I don't expect Navigraph to fix it in a hurry.
Cheers,
Martin