Pressure-fed engines are the simplest liquid-fuel engine design [1]. SpaceX's Raptors' full-flow staged-combustion cycles are massively more complicated. Yes, keeping your helium from boiling off is...a job. But taken as a system, the Raptor is more complicated.

> methane may be technically less capable, but much easier to work with

Also less precedented. Hydrazine/helium thrusters are amply studied. On technological risk, methane is untested.

> Steel is worse than aluminium in many ways, but it's also strong and easy to manufacture

It's also heavier and corrodes.

In summary, SpaceX chose a more-complicated engine design, a novel fuel and an unprecedented structural material and beat Boeing to the punch. In part because Boeing sucks. In part because Starliner has been obvious fuckwit fodder for at least half a decade, and that leaves you with a special sort of person who is willing to work on it.

> where the shuttle was famous for having a complex (but well engineered) sophisticated avionics system, SpaceX use "commodity" computers running Linux

The Space Shuttle's main computer was a System/360 descendant [2]. Its design philosophy implies that they would have used Linux were it an option.

[1] https://en.wikipedia.org/wiki/Pressure-fed_engine

[2] https://en.wikipedia.org/wiki/IBM_System/4_Pi