If that study was of submariners, is it possible long-term high-level exposure causes the body to adapt?

I am suspicious of 0.1% having a significant effect though, given oxygen is around 20% and we naturally exhale a couple of percent CO2.

I mean that can't be right, as the body's breathing response is triggered by that amount of CO2 buildup. It's not about what's in the air. It's about what the body can take up. Maybe submariners are self-selected to be more physically fit, e.g. larger heart, lung capacity etc. to compensate.