Honestly most bad startup organizational or engineering decisions I've seen were due to focusing on personal pet peeves and hatreds rather than logic or risk understanding. So I try to not do that.
Yeah personally I hate JIRA. I have no idea why their cloud is so slow for SELECT statements with 10 items, field config incomprehensible, or features randomly churn on weekly basis. That being said we evaluated other options as a team and were not convinced that the newer tooling was worth it. Our plan B was to spin up Bugzilla since we leave the project/task management process up to each team. If anyone has seriously found something better we'd love to try it out.
Your startup will probably fail because the product sucks and the founders suck. Whether you use JIRA or Trello or a sticky note on your monitor is utterly irrelevant.