Hi. Yes it definitely doesn't work when hotplugged, but I've had the Apple Thunderbolt -> Firewire 800 dongle installed/inserted throughout the whole testing process.
One thing that is slightly glaring is under IOThunderboltController in ioreg for the MacbookPro 11,2, there is a node called IOThunderboltport@5 (8086:156d). This is missing from my ioreg. In my system I believe this device ID is 8086:1567 (6 of them show up in DPCI manager).
Perhaps also have a swap for device ID 1567 to 156d is necessary in order for Thunderbolt to work? Attaching latest system.log, ioreg + macbookpro11,2's ioreg.
Cheers