More importantly, they're also built into the price estimate already, so when it says "$999" or whatever, that's including four $9 cards. It doesn't cost you any more to switch some of them for USB-A's instead, and other choices like HDMI, Micro SD, whatever, will be an upcharge.
A more savvy (sneaky?) approach might be to say that 4 cards are included and then only quote the increase over the base price for the things like HDMI that cost more, but I suppose they wanted it to be seamless in terms of how the pricing appears if you want to order more than 4.
Obviously there's a real sense in which engineering went into having this system and the things take up space, so there's a cost to having them, but I don't think calling them an upcharge is really legitimate; they're built in to the quoted prices.
I was looking at the DIY edition and the price is not included in the estimate so it is an increase in price to get any modules. Looks like you are looking at the prebuilt options and I see those do include 4 type C modules in the standard configurations and price. I think they should do the same for the DIY editions and let you remove them if you want.
That said they may be planning for a situation where you bring your own modules or buy from a third party if you wish -- it is an open design after all. Consider the enterprise use case. An org could have a batch of USB-C modules for replacement that they source from a third party for a cheap price, and then order the laptops themselves on demand.
Framework is all about reducing waste, so only giving users what they ask for is part of that.
It only reduces waste if mainboard/laptops are discarded due to a failed charging port. Does that happen often with type C connections on mainboards?
Unless they've done research that shows the type C port on the main board is a common point of failure and needs soldering to fix I don't see the point. I've had to clean lint out of ports but I've never broken a type C port on a computer.