So why didn't the Pentagon just say "Look, there's a perfectly rational explanation for these images"?

Why bother? This just diverts those pesky UFO freaks from revealing technical capabilities of our airborne sensors to potential rivals, and it draws attention away from anomalous sightings they are REALLY interested in keeping under wraps, like our ability to observe (or fail to observe) genuine terrestrial threats to US national security.

Strictly speaking, this is not a "debunking". These guys don't claim they know the ABSOLUTE TRUTH (upper case, in case you missed it). They just point out there are perfectly ordinary circumstances which could have resulted in the same observations.