By context, I have usually understood that "reference" means the system the speaker or writer knows best so as to be able to gauge other pieces of gear and recordings etc. It's not specifically a superlative but presumably people go to their best setup for that.
Manufacturers use the term as a kind of superlative. It implies the buyer will add it to their reference system I assume.
People that think their system is "a" reference system rather than "their" reference system...well that is a different discussion I choose not to start today.