Thinking about it a bit more, the actual/physical aperture of the 100-400 Mark ii at full extension could be something like f/5.9...i.e. above f/5.6 but closer to f/5.6 than f/6.3...and it might not really be 400mm as others have suggested...so taking those two things together it is possible that 100-400 Mark ii at full extension might have the very same physical aperture as the RF 100-500 at that focal length.
Edit in italics for clarification
Probably not, but they're close.
They are rounded down (marketing) so at 1/3 stop intervals something listed as f/5.6 will have a true f value between 5.657 and 6.350
At 1/2 stop intervals the f/5.6 range is 5.657 to 6.727
So, as the EF 100-400 shows f/5.6 at 400mm even on 1/3 stop we can be sure that the actual f value will be between 5.657 and 6.350
Looking back at the EF 100-400 patents (I'm not entirely sure which one is the correct one for the II) shows the f stop at 391mm (the real maximum) is either f/5.8 or f5.85
On the RF 100-500 at 400mm it has to be between 6.350 and 6.727 - which means you're probably looking at around 1/4 of a stop of light reduction - maybe less (especially if you measure at 391mm instead of 400mm).
In any case, the increase in light at the wider range of the lens plus the longer reach and faster focusing surely makes up for this!