Sure, but startups are an unusual case. Very few programming jobs are for startups. Most are for established companies that already have the business side down; where you are going to be too far away from "the business" for your experience to have any use. They need programmers that can add features in such a way as to avoid needing 50 new QA testers and overnight support staff. "Architechture astronautics" are fine; the company has plenty of time and money to invest into better solutions than whatever would put out the fire right now.

I've worked at small and large companies, and this has always been the case. The business was already well-established and does not really need help from the programming team. The programmers just need to craft extensible and clean solutions that solve the current problems and the anticipated future problems.

Startup experience wouldn't count against you, but neither would being able to run a marathon. The reality is that neither skill will be particularly useful. Being able to prove that you've written software, however, is a useful skill.

(People on HN seem to think that "good software" == "software that makes money", but that's not necessarily true. Good software products made money because of good marketing, good customer support, and general good business skills. The actual code quality varies. Ever use Windows? Yeah.)

Also remember that the OP is applying for a "junior developer" position, and I am answering with respect to that. CTO is very different from "junior developer".