The difference is - Eugenie's patronages are her own business and she is doing so as a person with enough fame and time to have an impact. The "working royals" do so on behalf of the crown and country. Beatrice and Eugenie have jobs and choose to support a few key causes close to them, just as Zara does (she is patron of Inspire, Lucy Air Ambulance, Sargent Cancer Care for children, Cancer Research UK and the Mark Davies Injured Riders Fund) or just as Lady Sarah Chatto does (she is Vice Patron of the Royal Ballet)
Only working members of the RF get their duties and work paid for, Eugenie and Beatrice have jobs that presumably pay them as well as trust funds from their parents and grandparents from private income. The late Queen may well have contributed something to them, a personal allowance or similar but if she did it will have come from the Duchy of Lancaster income(effectively the sovereign's salary and working expense account rolled into one) or her own more personal income. They do not get to claim expenses from the public funds for what they do. Simple as that. If they want to support a charity or attend a charitable event they o so knowing they have to be able to afford to do so out of their own pockets (which Im sure are deeper than yours or mine)
I think for a long time all working royals have been permitted a certain leeway in taking on some things more personal to them, but really how is that different from choosing what regiment to be honory colonel of or which royal institute or society one member of the RF should take on over another because they are more interested in it? As long as its doing public good / not for profit it is permitted, probably because it gives that working royal something interesting to look forward to amidst a large programme of less personally interesting things. The difference is most likely that if the government of the day or the sovereign felt a personal interest organisation taken on was inappropriate they would/could order the working royal to stop being linked to it but couldn't do so with Eugenie or Beatrice if it was personal (not saying the public or media pressure wouldn't make it untenable)
In other words, the working royals are public servants who do a whole host of duties and work with a whole range of charities of which a small handful may be more personally interesting to them, just as an ambassador or MP may be particularly interested in culture, science or fashion and build that into their official programme where it is supporting their country's interests. Members of the RF are private persons who can, just like you or me, choose to support any old charity or causes we want in our own time. When I do so I don't act as a representative of my employers or my family I do it as an individual, so are Beatrice and Eugenie.
