Can the OS X Mail dock count be made to show all (not just unread) count of inbox?
DockStar solved the issue for me. It now has an update to support both Mavericks and Yosemite when it comes out. I only tested in on Mavericks though, works great.

The great thing for me was that I have exactly 4 inboxes, so I can add a badge for all of them.