Quite possibly the sensor IS more expensive to fabricate, using as it does smaller circuitry sizes. Or it may make no difference; I don't know if the same foundry makes them both with the same equipment. But you do have to amortize development costs, too: the R5 is the first camera with this sensor, the R6 is using a previously used sensor.OK, how is the sensor cost different? The die for each is the same size, I am assuming that they are both made on the same fab line, in the same process node, etc. In which the cost won't be much different. Semiconductor cost is determined by the finished cost of the wafer divided by how many chips you get off of it (with adders for packaging, test etc.). So, if the finished cost of a wafer is $2500 and the yield is 25 chips then the cost per chip is $100 whether is has 25 MP or 50 MP. What you charge for it is a different story.
I still maintain that an EOS R6 and an EOS R5 are almost identical with a few differences (some of which I listed). I don't think there is a $1000 difference. That doesn't stop them from pricing it that way -- assuming that the customers will pay it and the competition doesn't come along offering something as good for a lower price. This appears to be what happened to the EOS R. I am guessing that there is room to move in the R6 as well.
Here are a couple different questions: Would they have priced it higher if the higher definition video modes actually worked well? Also, what is the use case for the video as it is? If you can only shoot for 20 minutes (and even that is qualified), after which you have to power the thing down and let it cool for 2 hours (?), in what situation is that actually usable? Can you still shoot stills if it has overheated like that?
But that's not the only aspect of it; you have to be able to handle more data, more quickly in the R5 than in the R6 (and that, indeed, is part of the overheating issue), which requires more processing power, likely more memory for the buffer, and on and on and on. And this will more than likely apply to the autofocus system as well. It's not just a matter of dropping a different wafer onto the spot that says "put sensor here."
I had no difficulty ponying up the extra cash for the higher-res sensor, video modes or no video modes.