As Rhiannon says, far more ridiculous assertions than that get passed off as fact in the wonderful world of megalithic ponderings!
My personal opinion, subject to the stone not being a later insertion, or moved (as per ED's question) is that it is far more likely than not to have been chosen by the builders. These were people very very aware of the textures and properties of stone after all, far more than we are. Not people to miss a whopping great big ammonite, no matter how many modern visitors don't spot it :)
Could they knap flint in a way that would put our best craftmen to shame, given what they had to work with it's a definite yes, but give me a modern powered saw and i'd make them look like imbeciles in comparison. Just look at some of the knapping slabs available to buy today if you've any doubt !
As for natural features like the ammonite, yes i guess they'd appreciate it more than we would today as they don't have the availability and distribution networks we have to source such pieces, so damn well it was precious, but that's no reason to assume they had a greater understanding of stone, they didn't, it was more a case of greater toil and time consumption, need even, that doesn't equate to skill.
You give me a 10p sized shitty bit of flint and i'll knap an arrowhead that will kill anything just as dead as their pieces could. :)
I've an arrow besides me right now, Wiltshire flint point held in place with pine resin, willow shaft and fletched with a buzzards feather found on Waden Hill, glue is crushed Bluebell bulb, binding is nettle cord. Match that with one of my bows and i could, with practice, match any Neolithic hunter. I respect their use of material, but let's not kid ourselves they were superior in ANY way, they weren't. IMO. ;)