For anyone that was interested.
It's not really FIM that SharePoint uses. It's a section of the ILM 2007 product (ie the last generation FIM) that's used.
1) The main advantage to integration of the two is that you only need to "change once" to include or update a connection. You can also, assuming your management agent supports it, do two way synchronisation.
2) It might or it might not, i never got a good answer.
3) There don't appear to be many connection agents out there, the userbase is small and the companies that make it don't seem to package them as user configurable. They expect that you'll bring in their consultant to install and configure, this drives up costs a lot.
As you might have guessed we're going with integrated.