Elroy,
Your question is essentially a 2 part, 2 situation scenario. One relates to the climb gradient required for a given obstacle, the other pertains to assesment of obstacle clearance if the aircraft is at a fixed gradient.
(1) "Obstacle height is generally referenced to the elevation at the end of the TODR." - Consider a 2000 M Runway of Elevation 1000 ft AMSL, Slope is 1% Down, and there is a 1100 ft AMSL obstacle at 1000 M from the runway end. As Elevation (1000 ft) is quoted for the highest part of the airfield, at the beginning of the Takeoff the Elevation is 1000 feet, and at the End of the Down-Sloping (-1.0%) Runway, the Elevation is 65.6 ft lower, i.e. 934.4 ft. To clear the obstacle the aircraft must climb from 934.4 ft to 1100 ft (165.6 ft) in 1000 M, a gradient requirement of 5.05%.
Now consider the opposite Takeoff direction of the same runway, also with a 1100 ft AMSL obstacle at 1000 M from the runway end. At the end of the (UP-sloping) Runway the aircraft is at 1000 feet, leaving 100 ft to climb to clear the obstacle in 1000 M. That's a gradient requirement of 3.05%.
Thus, for the same obstacle data, the Gradient REQUIRED from the Down Sloping Runway is 5.05%, Vs 3.05% for identical obstacle data from the Up Sloping runway. That's why obstacles are referenced to the lowest portion of the runway, and, in assessing Obstacle Limited Weights, a higher Takeoff Weight is possible from the UP Sloping Runway.
(2) "Assuming the climb gradient is constant, the flight path of an uphill slope runway will begin at a relatively LOWER elevation relative to a downhill slope runway." Now consider an aircraft at the WAT limit, unaffected by Runway Length or obstacles. In either Takeoff direction (assuming no wind), the aircraft will have an identical Climb Gradient, say, for example, 6.0%. The assumption is also made that the overall terrain in the area is the same as the Runway Slope.
For Takeoff from the Down Sloping Runway, the aircraft is achieving 6.0% to the horizontal, but 7.0% to the terrain, thus, at any point along the flight path, clearance of the assumed obstacle-free terrain will be 7.0% of the horizontal distance flown.
For Takeoff from the Up Sloping Runway, the aircraft is achieving 6.0% to the horizontal, but only 5.0% to the terrain, thus, at any point along the flight path, clearance of the assumed obstacle-free terrain will be 5.0% of the horizontal distance flown, a LOWER terrain clearance.
Some of the words in the quote that you made must be examined carefully. the words "relatively LOWER elevation" imply HEIGHT (above obstacles), by inclusion of the word "relatively", because all obstacle heights are assesses RELATIVE to the Runway Elevation.
Regards,
Old Smokey