The doctor is giving you the standard excuse when uncomfortable with actually treating hypo patients adequately to relieve symptoms. Since such clinical treatment frequently results in suppressed TSH, and a Free T3 that is in the upper part of its range, the doctor blames the wrong things. I think you can get some better insight from this letter written by a good thyroid doctor for patients that he sometimes consults with from a distance after initial personal evaluation. The letter is then sent to the participating PCP to help guide treatment. Specially note the discussion about causes of bone loss.
http://hormonerestoration.com/files/ThyroidPMD.pdf
I would push the doctor to test all the possible causes of bone loss and identify which areas are deficient.
Thank you for the post, this is what I suspected and I just wanted to make sure. What kind of doctor would you have treat this bone loss?
There is no specific doctor to treat osteoporosis. The best I can offer is to read this link and consider the suggestions there.
http://www.webmd.com/osteoporosis/osteoporosis-specialist