An innocent proxy?
As I recall, blanking or replacing the user-agent string is a standard feature of Squid (and presumably other proxy servers as well). OpenBSD's pf firewall has a "modulate state" option, which does something similar on a TCP/IP level (randomising all the parameters, making it hard to identify the OS generating the traffic).
If I wanted to hide my secret OS/browser, I'd have it report itself as something like a Subversion build of Firefox/Gecko running on WinXP - looking normal in logs, while having an obvious explanation for any odd behaviour server admins might notice (it's a work-in-progress version of an open source browser, of course it's not acting in exactly the same way as the last released version!).
Blanking the user-agent, on the other hand, would make sense in two ways: first, as a paranoid sysadmin wanting as little information getting out as possible (so you blank user-agent and probably have a firewall randomising parameters too) - second, to help catch sites which are running spider-traps which serve up pages of link-spam to anything other than IE. (In fact, the comment about these 'appearing to be real people not spider activity' could be exactly the point: comparing the pages seen by real people - and their proxy - to the pages served up to Googlebot.)
Or option 3: they don't want the world knowing that for all the hype about using 'Goobuntu' and having their own web browser, 90% of their staff are still using IE 7 on XP!