How is it determined that two cancers in body are a genuine metastasis case and not two individual cancers ?

A biopsy: can show which each is. In some situations it depends on the characteristics of the cancer. For instance, Breast cancer does not metastasize to breast. So if a woman who has breast cancer now gets cancer in her second breast - that should be another primary.

Cancers : If they are both biopsied, it is easy to tell, by the tissue types. If they are not biopsied, your doctor is most likely going by clinical experience. Good luck.