Her eyes were not deceiving her. The director of the Royal Botanical Gardens, Kew, William Thistleton-Dyer, had appointed the first female gardeners that same year. They wore the same uniforms as the male gardeners, as seen in this picture from the Kew Library website.
It is possible that the women Beatrix spotted had been trained at the Horticultural College for Women at Swanley, Kent established in 1889. The Kew Journal of May 1894 had an interesting take on possible hybridization:
"Cannot some arrangement be made whereby a Kewite and a Swanley Miss can join their forces and thus be a source oIf strength to each other? We might then have gardeners offering their services for the outdoor department, wife to take charge of the orchids and fruit, or a woman gardener might undertake to manage a large garden, her husband to act as foreman. Kew and Swanley should certainly have a special attraction for each other. Double-barreled gardeners would be an advantage, and their offspring would be born gardeners; but alas! gardeners as a rule are forbidden to have offspring."
As far as I know, this never happened.
Beatrix Potter never gardened at Kew, but she consulted with them and used their library. And she did take up the idea of gardening on her property in the Lake District, even if not in knickerbockers.