I'm not sure we could ever say it was 100%, however the bones were entwined and mixed up with the steel belting from the tires, implying that the body was burned along with the tires, however under cross-examination, the forensic scientist does not believe the bones had been moved from another site, to Avery's burn pit. Mostly because the bones themselves would have exhibited signs of being moved - as she explains in her testimony;
(Page 33, Dr Eisenberg )
https://static1.squarespace.com/sta...67/Jury-Trial-Transcript-Day-14-2007Mar01.pdf
This also aligns with Brendan's confession, where he explains how they used tires to help burn the body - again, information from the confession that lines up with how the remains were found.
What's interesting from her testimony, is that they don't just find big bones in the burn pit and barrel - they find tiny pieces of delicate remains, ash and charred flesh - which would imply that if she was burned at a different location - whoever transported her bones, must have done so with an insane element of detail - because it included all of the tiny complex bones and bits of skeleton, including things like teeth.