A PCIe x16 slot doesn't necessarily have 16 lanes.
As far as I can tell from their website, "Signal" means how many active lanes there are per connector, while "Output" means the physical connector size.
The picture of your riser shows three mechanical x16 slots. Furthermore, your provided part number is designed to work with this board which provides 32 lanes through its riser connector.
Based on this information, I would therefore conclude that while the riser has three mechanically x16 slots, they are not all electrically x16. One connector has all 16 lanes, and the other two have only 8 lanes each. This gives a total of 32 lanes.
It is perfectly fine for a connector to have fewer active lanes than the size of the socket. All PCIe devices are required by specification to work in a x1 mode, as will as one or more xN modes.
If you plug in a card that is designed for x16 mode, it will still work in the x8 slot, however with fewer lanes enabled. In many cases it will operate in its fallback x1 mode which is the only mode it is required to support.
In many other cases, e.g. lots of graphics cards, it will work in a x8 mode quite happily.