It appears to me that when running one of it's batch operations, the AHBot causes a large database load and prevents the core from querying the database in a timely manner.
It could even go so far as preventing it running queries all together, but I don't believe it's that severe.
I personally see no reason that the AHBot needs to be part of the Core. It has just about nothing to do with the AH Handler and Manager.
It doesn't really appear to make any significant changes to the MaNGOS code, just adds a couple of tiny customizations.
The way that I see it, and I don't want to belittle Xeross and everyone else working on the project because I love this particular addition, but having it as part of the core is simply clutter. It could just as easily be built as a separate process.
But that's my opinion, and as I'm new to this I may have missed something important.
Edit: As I failed to make clear above, it's not the Auction House that requires it's own server, it's the AHBot pummeling the database with thousands of queries that causes performance issues, and they're only intermittent.
The Auction House itself, in my opinion, is best off staying in the core.