I suppose this sort of behavior would be rare in a DC-DC flyback, since normally the flyback voltage on the primary side is roughly equal to the input DC voltage. If the flyback voltage is much greater than Vin (as is the case with a PFC flyback near zero crossings of the AC line), then I can see this becoming an issue.
I ran your sim, and there are times where the secondary side diode ringing does take the rectifier close to forward bias (it crosses zero, but not enough to really forward bias it), look around 1.42ms. However the LT8309 doesn't react to it. Even if I decrease the snubbing to make it worse, I don't see an extra pulse ever coming from the LT8309. Never used the chip, so I'm not sure how easy it is to fool.
If you intend to operate in BCM, then why are you worried about this?