You are operating on a false dichotomy that the current best practices of cryptographic security, code auditing, etc. are somehow mutually exclusive with obscurity, and then arguing against obscurity by arguing for other good practices. They are absolutely complementary, and implementing a real world secure system will layer both- one starts with a mathematically secure heavily publicly audited system, and adds obscurity in their real world deployment of it.
If there are advantages to a closed source system, it is not in situations where the source is closed to you and contains bugs, but when closed to the attacker. If you have the resources and ability to, for example, develop your own internally used but externally unknown, but still heavily audited and cryptographically secure system, is going to be better than an open source tool.
If there are advantages to a closed source system, it is not in situations where the source is closed to you and contains bugs, but when closed to the attacker. If you have the resources and ability to, for example, develop your own internally used but externally unknown, but still heavily audited and cryptographically secure system, is going to be better than an open source tool.