They are probably natural, but along the Avenue there is another large triangulate stone opposite its male counterpart that also has 2 large cupmarks nearer ground level. Its in a photo taken by Jaquetta Hawkes, the old b/w photos always shows up more interesting detail that digitals never do.
And, very rare for down south, but we have a megalithic stone with concentric circles, see Rhiannon's link at Knowlton Henges, it was found in the south henge. Plus, of course the "footsteps" stone found up on the Mendips at Pool Farm.

In Stan's 1999 book "British Prehistoric Rock Art" there's a map of south east England & Wales. The West Kennet Avenue (not the Long barrow) is marked on his map but there is no reference as to why in the text.
The Pool farm cist cover is not a million miles away as are Cairn Down & Bradbury.
I think it's gonna be a case of the more we look the more we find.
An example of this is, Stan's book doesn't claim to be a definative guide or gazetteer but he only he lists 8 sites in Wales, compare this to Darvill & Wainwright's 2002 survey that had a list of 33 sites comprising more than 37 panels in Wales.
For a while I was convinced I could see cup marks on the Devil's Arrows but I haven't been down there for a while so now I'm not so sure.