That's been the standard for the higher-end Yamaha models of keyboards and synths for many years. In fact, there are usually at least three manuals, the third being the Data List that has all of the details about the voices and MIDI messages and parameter values. There are also smaller documents such as how to connect to your computer or smart devices, but those generally aren't targetted at specific models like the manuals.
When I've gone to other company's sites, such as Korg's or Roland's, they also typically have several manuals, guides, and other documents for each model, so it isn't that unusual for Yamaha to do it. Even non-musical equipment, such as all-in-one printers, typically have multiple documents instead of one single manual, so the practice isn't limited to musical keyboards.
Anyway, for higher-end Yamaha keyboards the Owner's Manual is more of a quick guide that gives a brief description of the keyboard's features and the basics of how to use them, whereas the Reference Manual goes into more detail about everything-- except, as I said, there's also a Data List that lists all of the voices, styles, songs, arpeggios, and so on which are built into the keyboard, as well as all of the MIDI messages it recognizes, including System Exclusive messages, along with the parameters and their values.