The Framework laptop expansion cards are all USB-C dongles in a different form factor. It's purely an esthetic choice. You don't like the dangle. Thats a valid opinion. I have a USB-C hub that handles all the connections I need in a dongle-dangle.
The only real objective benefit of it, IMO, (and this is HUGE) is the repairability. I am a huge fan of that, and hope that other makes would step up (or be forced to step up) and make the same kind of changes.
The distinction between USB-C and PCIe, on the other hand, is meaningless for most peripherals.
An imaginary handheld AM radio is more similar to a handheld FM radio than the handheld FM radio is to a desktop FM radio, from the user's perspective. You could say that "comparing AM to FM is apples to oranges", but the user wouldn't care as much as they care about how they actually interact with the thing.
Are PCIe cards just dongles in another form factor? Is it a question of how much of the peripheral's surface area is visible from the outside? Or is it the difficulty of insertion/removal that separates expansion cards from dongles?
For me it's the dangling that makes the dongle a dongle.