This is a matter of debate among experts.
Whilst it is absolutely ok to use vaginal estrogen alongside systemic, my personal view is that if someone has a healthy level of estrogen in their body, their vagina shouldn't be atrophying, unless there is another condition eg neuropathy or poor blood flow due to previous surgery, radiotherapy etc.
Studies were done in the 1990s on plasma estradiol and VA by Sarrell et al, which found it was much more prevalent below a threshold level of 50pg/ml, and less common as women got above this.
(Note US units used. UK measures in pmol/L)
I find it biologically implausible that my vagina would be uniquely withering whilst every other tissue in my body thrives, and the likelihood is if one organ is protesting, my bones, heart and blood vessels etc are probably not optimally estrogenised either.
Whilst I realise that some of the very small risks associated with systemic estrogen are avoided with vaginal therapy, I am also slightly uncomfortable with the practice of only treating, or only treating adequately, the part used to potentially have penetrative intercourse with men, rather than the woman as a whole.
My view on this may be coloured by personal experiences and I am in no way suggesting vaginal estrogen isn't an extremely valuable therapy or that anyone shouldn't use it.
At the very least though I believe the ongoing presence of VA despite systemic therapy should prompt a review of the dose/absorption, that way you can make an informed decision whether or not to increase, with or without vaginal estrogen.