Blood tests for estrogen typically look at total E, which is often (though not all docs ask for this differentiation )broken down into E1 (estrone), E2 (estradiol) and E3 (estriol.) See
http://en.wikipedia.org/wiki/Estradiol for a discussion of the differences, relative strength and the place of each in the female reproductive cycles. Typically, endos are looking at E2 with the idea of getting the levels for MtF transsexuals into the normal range for females.
Blood tests for Testosterone and DHT are often also done for obvious reasons, though for reasons more to do with cost of the test (typical blood work for a MtF can easliy be in the USD$ 150 to 200 range without adding a test for DHT), DHT levels are often not determined since if free testosterone levels are low, DHT will be low as well.
Of course it is theoretically possible to test for the active ingredients in PM, but I have not read anywhere that it is done, and it certainly is not part of the usual panel of tests for serum hormone levels.
Since most endos use serum estradiol and testosterone levels to judge the "effectiveness" of a MtF HRT program (as versus actually judging the degree of feminization), and PM does not contain estradiol nor does it increase natural estradiol production, to a traditional MD it is "ineffective." Obviously, this does not mean it is not highly estrogenic (it is a highly potent estradiol mimic) or that it will not produce results in men (it obviously does for some men!), just that it does not affect serum estradiol levels. If the docs would take a minute to even begin to reason out what the standard hormone profile tests show with respect to how phytoestrogens work, they too would be able to see the error in their reasoning. Furthermore, it has long been the orthodoxy, dare I say dogma, that herbal or natural feminization is completely ineffective. In truth, they are partly right, lower potency phytoestrogens ARE inadequate for the purposes (and the time frame; oh they are an impatient bunch! lol) of most MtF transsexuals. However, it is my belief that this dogma was established in western medicine before PM became known, or widely used.
So the long and short of it is most western docs think phytoestrogens are all alike, and since soy is largely ineffective for MtF transition, they all are. Blood tests can not at present show what anyone has been taking to grow breasts or feminize themselves, even if they were using prescription hormones. The standard panel of blood tests merely tests for serum levels of the key sex hormones and nothing else.
Hope this helps.