I work for a medical device manufacturer, and software absolutely can be designed to be just as reliable as physical systems, but the development and testing process looks completely different than a developing a mobile app. Things slow WAY down: if you want to change one line of code, it'll take literally weeks before it makes it to a production environment because of all the testing, documentation, justification, and human approvals. I imagine flight safety systems are subject to a similar level of rigor.

This is a safety standards issue not a "software" issue. Standards for airplane software are very high

Most planes have been fly-by-wire for decades and aren't regularly falling out of the sky