PCR has worked on single cells, though admittedly I have found that difficult. I don't have first hand experience with PCR from urine, but assume thousands of epithelial cells from the urogenital tract would be recovered. Perhaps an MD might comment on that.
I shouldn't speculate, but I would think it unlikely that exogenous cells would make it into the urethra, and if so would be vastly outnumbered by endogenous cells. Still, it seems it would be prudent to clean one's self before submitting a sample. A mixed DNA fingerprint would suggest tampering. For example, one could add some of your own DNA into someone else's urine. The mixture would be apparent. So an innocently providing a mixed sample (i.e., having sex, then submitting a urine sample) could look pretty bad.