Elevations - RTK vs Levelled

the observed RTK elevations were based upon just two or more 3 second observations.

The rover unit employed has the tilt sensor feature. That feature relies on an IMU, which must be kept mostly in motion to stay calibrated. So you can't linger over a point for long - unless you turn the tilt sensing off.   

Which constellations were you observing? Makes a difference for what you’re stating. And turning off your IMU probably would have made for a better test since a good rod vertical is better than tilt/IMU for control. IMU is a tool for safety and non accessible objects and topo points.