A CT scan can't tell if a growth is cancer or not (although if there are multiple or irregular tumors, it's a good guess.) How do they know it's metastatic bone cancer? You mentioned the 12r lymph node was negative. Was 4r positive? Was the benign cyst the only lesion on your kidneys?

A CT scan with a contrast agent, I presume? Those are very hard to interpret. I just had one for routine monitoring of my stage-4 prostate cancer, and it's down to the skill of the radiologist to look at increased uptake in an area and conclude that it's likely due to something other than cancer (especially if there's corroboration elsewhere in my medical chart, like bloodwork that contradicts cancer in that location).

In your case, I'm guessing it was inconclusive enough that they wanted to do biopsies to be certain. Not that they were convinced you had cancer, but that increased uptake of the contrast agent in those areas meant that *something* was going on, and they wanted to rule out cancer.