Unfortunately this has been on-the-job learning for me over the last few decades so I don't have great sources to point you to, but this is covered in systems engineering courses for aerospace and automotive applications.

Same thing with control-theory - there’s so much established knowledge out there that one really needs to know but which isn’t taught to kids in uni or even postgrad level. Learning these things on-the-job means you don’t know what you don’t know…

What’s a better way? We still don’t have state-regulation/certification for software in safety critical systems, which terrifies me when I think about it.

We have DO-178C for aviation, which (a) is a pretty good standard and (b) is a heck of a lot better than ISO26262. It's "voluntary", but it's the only game in town, so…