Yeah, the basic gist of how a stick shift works hasn’t changed that much since the Model A, but there’s still a certain amount of work that goes into making one that fits in a particular car. That still costs about the same as it always has, but as the take rate for manuals has plunged, they’re spreading those costs over a smaller number of cars. So the car makers have to charge more for each manual car they sell to make it worth having a manual option at all.
Increasingly, sub assemblies like gearboxes are not manufactured in-house by car makers but subbed out to specialists like Getrag. They make boxes for manufacturers world wide, many in countries like the UK where stick shifts are the more common. This rather counters the idea that a manual box will cost more due to rarity. Autos cost more because they are more complex.
As someone pointed out above - the price we pay for something is more to do with what the market will bear than the cost of manufacture, marketing and distribution