/home should remain untouched through any System76 driver operations.
As for System76 and support, I love the hardware and the people, but the repair process can be somewhat painful. I needed a new graphics card in my SerP7 and so was without my laptop for a time. Communication to update me on the progress was non-existent, and UPS was the only option for shipping.
FedEx is much much better for those of us that can't sit at home between 6am and midnight (I gave up at 11pm and went to the bar for a bit only to have a note on my door from UPS when I got home....ridiculous) waiting for UPS to deliver on the expected date. FedEx allows the recipient of a package to have it held at a 24/7 location for up to 5 days.
All of that said, my system was repaired and has worked flawlessly since. I fully expect to buy my next laptop from System76...
Apart from that, it just does the basic driver installation, like the Install function.
I'm always a bit surprised how sometimes Laptops resellers (not system76) might not want everybody to know that the buy barebones from Clevo ( or others) .
But let's Face it : there is no other way. even with 10K units/months , I'm not even sure you could afford your own plastic design etc....
The Clevo ODM model is a great choice and everybody wins, the machines are great and have a quality/price ratio unbeatable, the Bios can be customized for each customer etc....
on the other hand I think it's better if the "builder" tells explicitly that the machine is a Clevo XXXYY. it's easier then to find reviews or replacable parts.