OwnCloud actually has security issues similar to what you cited in the second link. Their security track record isn't spectacular either.
https://blog.hboeck.de/archives/880-Pwncloud-bad-crypto-in-t...
https://blog.hboeck.de/archives/880-Pwncloud-bad-crypto-in-t...
Only because a project is serious about actually publishing vulnerability data does not make it necessarily more insecure (or secure).
https://blog.hboeck.de/archives/880-Pwncloud-bad-crypto-in-t...
In the case of Seafile one could simply change passwords of any user etc.
But yes, crypto is hard and I agree that the way we did it at ownCloud is far away from the best way. :-)