I've watched the video several times and the portion at the 6:05 mark seems to me to do the opposite: he explicitly says that the larger entrance pupil will NOT be brighter because even though there is more light entering the pupil, that more light has to make up for the narrower cone.
Exactly, we can't ignore focal length and just think about entrance pupil when it comes to illuminating the image plane as focal length determines how much light is captured from the object side of the lens.
Consider two lenses pointed at a large uniform target with uniform illumination such as a very large evenly lit gray card.
The longer focal length lens integrates photons across a smaller area than the shorter focal length lens aimed at the same target. The longer focal length lens with the larger entrance pupil may do a better job of delivering those captured photons to the image circle but fewer photons were captured to start with.
Consider two lenses, a 200mm lens with a 12 degree angle of view and a 600mm lens with a 4.1 degree angle of view (reference:
https://av.jpn.support.panasonic.com/support/global/cs/dsc/knowhow/knowhow12.html)
At a fixed distance of 10 meters the 3:2 aspect ratio rectangular area captured by these two lenses are:
2.16 m^2 for the 200mm lens
0.24 m^2 for the 600mm lens
Field of View calculator:
https://www.scantips.com/lights/fieldofview.html#top2
When both lens look at a large uniformly lit and uniformly toned target (e.g. large gray card under uniform lighting) the 200mm lens captures 9 times the number of photons due to its wider field of view. (2.16 m^2/0.24 m^2 = 9)
So yes, the 600mm may have a larger entrance pupil but that alone does not predict which lens will deliver more light to the image plane. We also have to take into account focal length and that's exactly what Relative Aperture or what photographers think of as f/ stop does. It takes into account BOTH entrance pupil and focal length to determine how much light will be delivered to the image plane.
FWIW Shane, I agree with the results of your field test comparing the two lenses. Yes, doing this test at a fixed ISO was valid just as doing this test using film with its fixed ISO would have shown the same relative results. Similarly if you had access to a lab grade incident light meter and used that instead of the camera you would also have seen the same relative brightness results as the f/2.8 lens did in fact deliver more light to the sensor than the 500mm f/5.6 lens.
Physicists studying optics figured this and standardized the use of Relative Aperture (f/ stop) nearly a century ago. Since then and even today photographers use calibrated incident light meters to accurately predict shutter speed and ISO for a correct exposure based on f/ stop used and incident light. These meters do not typically have any direct entry for entrance pupil nor focal length but accurately predict appropriate exposure settings based on f/ stop as that takes into account not only entrance pupil but the angle of view of the lens and what that means for light gathering and delivery to the image plane.
I agree with the basic premise that when comparing similar long telephoto lenses the entrance pupil is one indicator of which gathers more light when scaled but you can do the same relative scaling with f/ stop in a way that may be easier for experienced photographers to grasp.
For instance comparing the 400mm f/2.8 (approximate entrance pupil of 143mm) to a 600mm f/4 (entrance pupil of 150mm) we could as was done in this thread say yup, when the lenses are normalized to the same field of view via a suitable TC (if we could find a high quality 1.5x TC) or via cropping the 600mm f/4 has a light gathering edge.
But we could get there based on f/ stop and focal length and come to the same conclusion.
400mm f/2.8 plus a hypothetical 1.5x TC yields a 600mm f/4.2 lens vs the native 600mm f/4 lens.
Same thing if we decided 800mm would be a better comparison focal length:
400mm f/2.8 with a 2x TC = 800mm f/5.6
600mm f/4 with a hypothetical 1.333x TC ~ 800mm f/5.33
Again it's easy via this f/ stop based normalization to see that the 600mm f/4 gathers more light even when both lenses are normalized to the same longer focal length and it doesn't require direct knowledge of entrance pupil as that is implied via focal length and f/ stop.