Arguably the difference is still the amount of resources Apple throws at the Macbook line compared to the amount of resources System76 throws at their computers. Truth be told I'd rather buy a Thinkpad or Dell XPS than a System76 laptop.
Apple has engineers dedicated to building hardware and software that work together. They design and manufacture their own hardware. System76 doesn't. They pick out some components, and get them assembled elsewhere, and ship that out to you.
A better comparison would be Dell's XPS line, which at least has some number of people actively working on making sure they work well and are well supported, but still not to the same degree as Apple, and my understanding is they're generally told "make this work with Linux", as opposed to building a laptop specifically for linux.
Apple has engineers dedicated to building hardware and software that work together. They design and manufacture their own hardware. System76 doesn't. They pick out some components, and get them assembled elsewhere, and ship that out to you.
A better comparison would be Dell's XPS line, which at least has some number of people actively working on making sure they work well and are well supported, but still not to the same degree as Apple, and my understanding is they're generally told "make this work with Linux", as opposed to building a laptop specifically for linux.