Mh, maybe someone can confirm this but for me this seems to be fixed with the latest update..
I updated my MacBook Air to Yosemite last week and - on my main Computer (still running Mavericks) I switched to Apple Mail some time ago (coming from Thunderbird) because i LOVE that conversation thing, so I set up Mail on my Macbook Air as well (was using Thunderbird here, still) - just to see that everything is messed up (had basically 600 mails in one large conversation etc) - doing research in the www I ended up here.
I was just about to swap back my system image with Mavericks today - because I am not sure if I like Yosemite at all ^^ - then I installed 10.10.3 - well, now it seems to work.. Hate "Fotos" btw... I am an Apperture user...
What I did was deleting the Mail Account yesterday, going back to Thunderbird - so I installed the update without a Mail archive - now i just re-setup an account and as it seems to me mails are grouped correctly now.. Btw - Postbox looks good to me!!