This is something that is asked all the time...
There are a lot of issues with this system and the comparison besides the
ones you have mentioned. It's not in the same class for starters. The system
ships with digital handcuffs, has privacy invasive enabling technology, has a
wifi card that is not compatible with Trisquel or any free software operating
system, and may or may not in fact include a graphics card dependent on
non-free software. System76 has in the past failed to disclose systems which
were actually shipping with NVIDIA graphics chipsets. I'm not sure why that
was although my guess is it was an oversight as they would consider such a
graphics card and advantage whereas we would not.
The biggest thing impacting the price is the size and weight. You will pay
more for a slimmer unit. The next issue is that the components inside make a
huge difference in the price.
As an example a low end SSD drive is likely to cost half as much as anything
that is remotely reliable. Where we avoid SSD drives that are near guaranteed
to fail within a year System76 may or may not. I haven't checked out the
components there shipping with recently.
If your after the lowest possible price and are willing to sacrifice
freedoms, quality, etc. there are cheaper systems out there.
We try and offer a reasonably priced basic system so users don't feel they
must go with a lesser system or less freedom-friendly system.
I also don't know if the hardware they ship with works with GNU/Linux. I
can't tell you about System76's support for GNU/Linux or free software
although because I haven't had as much opportunity to touch systems from
them. I can tell you though that others are shipping systems with GNU/Linux
that have unsupported power management features like suspend to ram amongst
other features many would consider critical.
Our systems aren't necessarily perfect for every customer (you'd never want
one for hard core gaming- but then again- your not using GNU/Linux for hard
core gaming either) although the support for GNU/Linux and free software is
pretty darn impressive.