Ah, but the Agency is only the navigation authority for certain rivers (Thames, Nene, Great Ouse and tributaries, Wye, Lugg, Medway, Welland, Glen, Ancholme, Suffolk Stour; plus a few oddities, like Lydney Harbour and Canal, Rye Harbour; and I'm not 100% sure of the situation on the Yorkshire Derwent or the Market Weighton Canal).
Though the Agency administers certain functions on all the rivers of England and Wales, such as pollution control, it doesn't have power to demand boat licences for them except where it is expressly the navigation authority.
Frouds Bridge is at least a fairly predictable case. There are, however, a handful of standard marinas on standard, BW-owned canals that are exempt from the need for licences, for no reason other than it wasn't required by any connection contract when the marinas were first constructed. I believe that there are some on the Llangollen, for example.