Just an educated guess but I am assuming the age of the wood is a good enough proxy to construction. Making the assumption that wood out in nature will decompose in short order (when thinking of the stated age). Being off a few thousand years is probably ok.

But somehow the wood is still intact 500k years later?

It was probably buried under anoxic conditions, which would weaken it and make it less suitable for new construction.

"Intact enough to be recognized" is a lower standard than "intact enough to be useful as a building material".

Kind of as other said, it was buried. From what I have read archaeological finds are about piecing together good guesses. Sure some wood is rot resistant but I suspect you would be hard pressed to find wood sitting outside for 1000+ years on the ground that early civilization would find appeasing to build with. Anything is possible but I am guessing it either fell natural or was harvested by those people and they decided to build with it somewhere plus or minus a thousand years.

From the Nature article posted by unwind, it sounds like they dated the sand surrounding the wood, not the wood itself.