It validates, it doesn't just scan
The key distinction, set out in NIST SP 800-115, is that a penetration test actively exploits a weakness to confirm it exists, rather than only reporting that a vulnerability might be present. That's why a good pentest cuts through scanner false positives: every finding comes with proof. The flip side is that it is a time-boxed exercise at a point in time. It reflects the system as it was tested, in the agreed window.