Estradiol will show up on blood testing, while phytoestrogens wont. So if you're having regular testing done, it's nice to be able to see where your E levels are at. Also, it's cheaper than or close to the same price(depending on how your buy your PM) of PM if you have a prescription.
Just to clear something up, estradiol is often referred to as "synthetic", but it's bioidentical to the estradiol found in humans. Phytoestrogens are found in plants but not humans "naturally". So an argument could be made that, in some ways, estradiol is more "natural" a substance to the human body than plant-derived estrogens are.
All that being said, if you don't want to go through the medical orthodoxy (which I don't blame anyone for not wanting to do so), have no issues with, and are getting good results taking PM, then in that circumstance it would be safer to continue taking it than to switch to estradiol, in my opinion. Even though I developed some side effects from PM eventually, if I had it to do over again I'd still start out with PM, as most have no problems with it, and it produced good results for awhile.
Nothing is ever truly safe though, or to phrase it differently, everything is safe until tragedy strikes and you are in that "1%". That's true of so many things though. Inherently, living your life is not a safe venture.
Good luck with whatever you decide to do!