We don’t know for sure that Silbury and the Obelisk were visible from each other when both were ‘in use’ but, assuming that they were, then anything goes really. Ceremonial use would be one possibility. Practical use as two points in a chain of beacons might also be a possibility. If you could see Silbury from other points in the Henge it’d probably be safe to say that the 'alignment' is coincidental, but the fact that it’s an alignment between Silbury and the Obelisk might suggest that it was intentional.
Speculating again, maybe it was/is possible to see Silbury from on top of the Cove; next time I see someone up there I’ll ask (then tell them to get the effing down ;-) On a serious note, you can see Silbury from Winterbourne Bassett and, at this time of year, from the road between Winterbourne Monkton and Avebury. Be nice (if it hasn’t been done already) to have a map showing all the points from which you can see Silbury.
It's hard to tell from this, Panorama 1, http://www.bbc.co.uk/wiltshire/content/panoramas/silbury_hill_top_1_360.shtml how much of Avebury is intervisible but some is. What you can see is how (apparently) deliberate the view of the Ridgeway is, over Waden.
I'm pretty certain you could see it from the vicinity of the Cove if the buildings weren't there but it's extraordinary difficult to work it out. Could the most significant sightline in the whole place have been hidden from us for hundreds of years?
Whatever, Silbury is all about seeing and/or being seen judging by the evidence IMO.
"In the South of England the common meeting place was Avebury, where the greatest prehistoric monuments in Europe are still to be seen. It is not unreasonable to suppose that this central gethering ground was the seat of government and its authority extended as far as the roads that radiate from it...". (The Green Roads of England; R.Hippisley Cox, Methuen & Co 1914)