The ability of the plant breeder to collect the royalties is in subclause 5(2):
Without prejudice to any rights or privileges of the Crown, an authorization conferred under paragraph 1(h) may be subject to a condition to pay royalty to the holder of the plant breeder’s rights whether or not the holder is Her Majesty....
If you go back up to paragraph 5(1)(h), dealing with the rights that it sets out for the breeder that the latter can give to the farmer, the rights are all about the production and reproduction of the propagating material of the variety and the selling, exporting, or importing of the propagating material. Then the farmers' privilege comes and it carves out those elements of propagating on your own farm for future use of the harvested material.