It's worse than you think: They are somewhat hamstrung in their hardware decisions by the current offerings from those Apple/Ultrabook chasing OEMs, but in this case they jumped the shark entirely and
removed the 2.5" drive caddy.
The nearly identical Clevo NL51RU/NL50RU [1] has a 2.5" drive caddy but a 36 Wh battery. Take a look at the internal photo of the System76 unit at [2]. It's the same laptop. Heck, they didn't even bother removing the boss and brass insert for the 2.5" drive retaining screw by the left speaker.
System76 is not an OEM, they whitelabel and have tweaks made to Clevo/Sager laptops. I think they do a great service to the Linux community with PopOS and driver development/compatibility to make those into machines where Linux "just works" out of the box, don't get me wrong.
This obsession with thin-and-light goes completely counter to the whole point of "Our laptops’ guts are fully accessible!". They say they've got a tactile keyboard, to fit in 20mm thin right on top of the heat sink for the high-power Ryzen processor and discrete graphics I think I'm pretty safe in assuming it's a pathetic 1" thick or more is not too much. You could fit in all the ports, as well as an 80 Wh battery, and cooling to run at boost frequencies for more than 20ms. You don't have to match the dimensions of a Macbook Air and be able to slice tomatoes with the wrist rest.
[1]: https://laptopwithlinux.com/wp-content/uploads/Clevo-NL51RU-... from https://laptopwithlinux.com/product/clevo-nl51ru/
[2]: https://assets.system76.com/products/pang10/internal.png