Why would a thyroidectomy final pathology report (not fna) be inconclusive (goiter vs follicular neoplasm)?

Second opinion. If after a thyroidectomy, your local pathologist still can't differentiate between goiter or cancer ask your doc to request the pathologist to send the tissue to a bigger referral institution for a second opinion.
On a continuum. The truth is that common nodular goiter shows the same microscopic pattern and some of the same mutations as do the tame follicular neoplasms. They're on a continuum. The burning question is really, "is this a malignant follicular neoplasm?" if the pathologist can say, "no", you're home free -- congratulations. Any concerns -- get a few more pathologists! good luck.
Medicine is hard. Nothing in medicine is ever black and white, and thyroid is notoriously hard to read. Your pathologist probably has many years of looking at thyroid and would be happy to call it if they could... But sometimes cells don't talk.