Definitely not a waste of time at all, the cream will still penetrate. My Vaginal Atrophy is well under control now and if I have a flare up it's totally down to my own actions, like treating myself to a nice foamy scented bath instead of using what's in the industrial looking containers that litter my bathroom now.
Once you get VA under control, it took me a year, flare ups are not too bad and can be relieved by an extra dose of treatment, go for it, there is no need to suffer.