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Just to clarify something when you're talking about the position attribute of trajectory points, are you referring to the position member of the trajectory message here? This is not the Cartesian position of the last joint of the robot but the final joint position, an angle in your case.

All the 6 DOF revolute arms I can think of often have several different joint solutions for a given end effector pose, so it's perfectly possible that different planners will end up with a different joint angle solution while giving the end effector exactly the same pose.

However you can use Moveit to define a goal in terms of joint angles instead of end effector pose, this means that the planners will all end up with the same (to within a tolerance) joint angles. The method you need is moveit::planning_interface::MoveGroup::setJointValueTarget

Regarding trajectory resolution, I don't think there is anyway to do this. The number of points on a trajectory is defined by the movement tolerance specified, and is calculated on the fly. There is nothing to stop you interpolating the different trajectories you generate to the same sample spacing though, It could get a bit strange if trajectories are of significantly different durations.

Finally, can you explain exactly how you're comparing the trajectories?