I don't know, but it could be that adding a later BA barrow to a earlier Neolithic one might have been viewed as a respectful continuation of earlier practices. After all, there are loads of long barrows where later round barrows have been built nearby in an obvious relationship (Belas Knap and The Crippets both close to where I live are the first two I can think of). Whereas a fort - whatever its purposes - may have been located primarly because of its landscape context, where an existing barrow might have been coincidental rather than deliberately sought.

Alternatively, placing a round barrow onto an older one (or into the side of a henge, like Arbor Low) might have been viewed as an assertion of power. I get the impression that Neolithic funerary sites respect the landscape more than BA barrows do. Long barrows are rarely built on top of the hill but usually down the slope (although Adam's Grave is a really good example of the exact opposite!), whereas many BA sites are deliberatly placed on the highest available point, as if to say "we are masters of this place".

I think we might have a better understanding if we knew how closely the people who lived here during the monument building periods were related/descended.