I would rather have 4 Thunderbolt 3 ports than 3 Thunderbolt 4 ports, an SD card slot I won't use, and 1 HDMI port that can only be used for HDMI instead of whatever the hell I need it to be another Thunderbolt port can be.
I would rather have a ThinkPad X9 15p Aura Edition, which has 3x thunderbolt, SD Card, HDMI, and USB-A, all at the same time with no dongle.
They also let you customize what ports you want in your laptop. You don't have to customize them. You don't have to pull them out. It's still an advantage.
You can also replace your ports easily if they get physical damage.
They can also be used on any brand of machine or even a smartphone. They're just Thunderbolt/USB-C.
They don't take space away from the battery, the battery on the Framework 13 Pro is almost the exact same size as the one in the MacBook Pro 14, and as of the M5 model the Framework 13 Pro gets better battery life than that Mac.
Because the Dongle-heads do have one thing right, one port that can be turned into lots of other kinds of ports with a dongle is more versatile than a port that can only be a video out, especially when the device doesn't have a ton of room for lots of ports.