If you use a framework like Laravel it probably covers most things.
You could easily write a massively insecure application in core python, but things like Zulip use Django which shields you from most of it.
It is not about the language is it... I don't think there is so big difference between php and python. Besides Slack is most probably using whole lot more tech than php.
It is about Zullip being open source.
It's also about the language. See, for example,
https://www.quora.com/Why-is-PHP-hated-by-so-many-developers
If you divide the amount they've paid out in bounties by the number of bounties paid, and compare with their bounty tier rules, it's clear that a lot of the vulnerabilities that were reported in Slack are relatively severe.
(And I agree bug bounty programs are great; we also use HackerOne)