All of the major Boston area flute makers produce handmade flutes. That includes Brannen, Burkhart, Haynes, Nagahara, and Powell. Several of them also sell mass produced flutes under different names. For example, Amadeus is sold by Haynes, Sonare is sold by Powell, and Resona is sold by Burkart.

Looking up the Powell Signature and the Haynes Q series...I think both of them only have a handmade head. It doesn't appear that they are completely handmade. And since there is a huge price difference between the Powell Signature and the Conservatory/Custom handmade flutes, I would assume that is correct. Same thing with the big difference in price between the Q series of Haynes and the Customs. Just adding that in
Personally when I got my first handmade flute, I focused more on Sankyo, Miyazawa, Murmatsu (sp check on those last two...as I never owned them). I ended up with the Sankyo and was very happy for many years.

I have a bog standard (equivalent to a now Yamaha 500 series) Yahama flute and a handmade headjoint. I just checked and it appears as if the company is no longer in business, so... I can't recommend it to you, but 90% of the sound is the headjoint. Spend the money there. It's entirely possible to get a custom headjoint on say, a lower end flute(ie - high-end but not handmade) and save a lot of money.