The Mac may have way faster storage. Or higher bandwidth RAM. Or run cooler. Or start faster. Or longer battery life. Or a better trackpad. Or keyboard.
Or not.
A lot of stuff in both machines is commodity parts. Apple doesn’t make its own screens and the Air is the worst screen their offer (I love it, but it’s relative). They don’t make storage chips or RAM chips or WiFi chips. A lot of stuff any company could do.
And, even ignoring the RAM/SSD prices, Apple loves their 30-40% margins. If Framework is willing to make less per machine they have more to spend on each unit even at the same price. Some of this is lost to volume discounts they don’t get, but it still helps.
They use 3rd party NAND and DRAM but the controllers for each are part of their custom SoC (along with their CPU and GPU) and things are a little bit different than how anyone else does it with integrated solutions as a result. I believe the USB/thunderbolt are part of their custom SoC too. Some of the microcontrollers for other functionality (secure enclave, camera/microphone processors, touchpad and the like) are outside the SoC but custom. Wi-Fi is still a standard Broadcom chip, for now at least :).
It's somewhat disappointing how much cool customer hardware is limited to just Apple products to be honest.
You’re right USB/TB interfaces are on the M3 (or whatever) directly.