My guess is a intake valve stuck open and when the cylinder fired it blew into the manifold. I had a back fire on start up a long time ago after the truck sat at the airport for three weeks. And again on the way out of the parking lot. Didn't break the manifold, but I think it was a close call.
In your case I would do a compression check before firing the next time.
Pulled heads had them redone no bad valves or springs did compression check before I pulled them good compression on all cylinders waiting on new intake I'll put back together and hope it doesn't do it again
That's a weird one for sure. Go a step further for good measure and replace the purge valve on the truck near the lower battery area. They have been known to sometimes stick open and on a refill of fuel get fuel in the line and sick that into the intake essentially making an injection bomb possibly. Changing that and having the heads done pretty much covers any possible issue