Hi Florian,
Unfortunately we keep seeing issues with Server Name Indication (SNI) even after we migrated Atlassian Cloud to Java 8. We are working on a resolution and will post here once we fully support SNI. For now, the best advice is probably to stay away from it, but we do understand that this is not always possible.
Cloudflare's SSL for Free plan relies on SNI, unfortunately, and that's why you get the SSL errors on installation.
One option is to upgrade to Cloudflare's Pro offering until we fully support SNI.
Regards,
Patrick