Research and development is probably very high when you consider Proton, SteamOS, and the semi-custom CPU and GPU. Something between $50 to $100 million would be typical. Silicone is famously expensive in R&D, Proton has continuous costs (and has for quite a while now) that rack up, and SteamOS is literally an operating system. That's a lot of salaries to pay.

I reckon they're taking advantage of being private and playing the long game. Very, very long game. They're not really in danger as long as Steam is successful, but I can't blame them for wanting a decent gross margin so they can at least cover hardware costs. Especially with memory prices right now, I wouldn't be surprised at 1000€ here in Germany, though I wouldn't be happy about it. I would happily buy at 900€ (≈$1040), and be ecstatic at 800€ (≈$920).