How to read BNF syntax of C?
Backus Normal Form does not define special syntax for %token.  So that would be a special syntax custom-added by a particular person or web page or tool.  Tool support is off-topic here, but if search for "%token" on the first link you gave, you'll find a brief explanation that appears to describe what %token means in the context of that particular example.

In other words: if you only want to understand BNF at a conceptual level, ignore it.  That's something that's not part of BNF, but is an add-on that was added for some special purpose.  If you want to understand that the specific syntax used by some specific tool (e.g., YACC), your best source is probably the reference manual for that tool.