True. Which is why the common perception that "hops cause estrogen effects" is also far too undifferentiated.
Being an expatriate Dutchman myself, I can tell you that the English and the Dutch didn't get along too well in those days, and that the Dutch diet of the time was also high in fat and starches. Interestingly, at the same time the Dutch had (and, to a certain extent, still have) the same opinion of their Eastern neighbors. (No offense!)
Strangely enough, facial lipodystrophy ("fat face"), if not caused by diet and/or as part of obesity, is primarily related to an excess of steroid hormones such as cortisol, costicosterone, cortisone and aldosterone. Phytoestrogen intake elevates none of these significantly; if anything, they tend do lower it.
But that's getting more into the medical side of things (and beyond my qualifications) than it is about brewing. So let me not digress too far. To return to brewing: hops replaced gruit for several reasons.
Gruit herbs, especially certain widely used combinations, were to a large extent hallucinogenic and/or had a significant stimulating effect, and were therefore widely used in pagan rituals. (Think druids cavorting naked in the woods during the Beltane fertility rites, and let your imagination take it from there!) This was the late middle ages when the Catholic church was on a mission to eradicate paganism, and suppressing the herbs required for pagan ritual went a long way towards that goal. Also, gruit tended to make the brew more potent and tended to cause more intoxication; it lowered the inhibitions and generally made for a much rowdier party where things got indiscriminate more often than not. Hops did not act as a stimulant but instead are a mild soporific, which means the party tended to end earlier before things could get out of hand so much. This suited Church leaders who frowned upon the frivolities induced by many gruit blends.
Also, gruit consists mostly of wild herbs that could be found and harvested anywhere, while hop was grown on farms as a crop. This made hops controllable and taxable, which gruit could never really be. The Church was after control, and taxation provides a means to control many things as well as provide revenue. This was yet another nail in gruit's coffin.
The gruit->hop transition also came at a time when the brewing industry was in the process of being regulated to protect the food industry. Since water was lethal to drink at the time due to widespread bacterial contamination (the idea of keeping your drinking water supply separate from your sewage had not gained much foothold yet) so beer was enormously popular. Anything that could be made to ferment somewhat was used for brewing, and grains for baking bread and the like became scarce, leading to excessive food prices.
So the time was right to put everything into one set of legislation. The Reinheitsgebot of the early 1500s killed many crows with one stone: it protected the food industry; it eradicated pagan herbs, it put a stop to excessive celebration, it allowed beer production to be controlled, regulated and taxed, and it put the Church in an increased position of power. And the rest is history.
Also, in a remarkable feat of marketing, all of this was sold to the population as purity legislation intended to ensure the quality of beer, and it has survived as such over the course of the next five centuries!
In short, while phytoestrogens are real and do have a place in physiology, their overall contribution to the perceived effects of having a pint are grossly overestimated. That said, brewing with gruit is fun and opens up a whole range of experimentation (pharmacological or otherwise). At the same time, hop just simply tastes good in beer. So we all win in the end!