First off what stage were you at when testing. Were they tests on estrodiol and testosterone done at different times and on a different cycles of your period?
If this type of testing is not done at specific times of the month at exactly the same time each time they test them, then stabbing at "lack of estrodiol" and over stimulation of testosterone is only a guess. Treatment could fail for you - if these tests are not looked at specific certain times of each time they are testing you.
Can thyroid mess up these labs?? Sure it can. The thyroid controls almost every aspect of proper body function and if it is running low - then a world of other hormones and conditions can be jazzed up and happen to you.
I first had my estradiol level ran randomly. The level at that time was 45, then they retested it on the 3rd day of my cycle and it came back at 42. My endo ran the estradiol and testosterone during ovulation because the estrogen level is suppose to rise during this time. This time it came back again at 42. Does this help?