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.