Thanks for all the detailed info. 
 
Interestingly, the synth rack also displays the BFD3 instance loaded into the FX Bin, the same as if BFD3 was inserted directly via the synth rack.  So is the main difference that inserting via the synth rack allows you to automatically create outputs per track?  (This would be reason enough to do it, as I've been pondering how to easily map each BFD3 drum's output to an individual track in Sonar.)  Or is there something else I'm missing?
 
 

Yes, any plug-in which has "Enable MIDI Output" turned on is automatically added to the synth rack. Some FX plug-in can generate MIDI data, they too appear in the synth rack when added to an audio track FX rack.
 
The main visible difference is the "Insert Soft Synth Options" dialog. I believe there are some other differences inside SONAR but I have no details.

Bristol_Jonesey
And welcome to the wonderful world of Drum Maps & routing!! (Unless you do it all inside BFD of course)

BFD3 sends the drum map to Sonar. No need to deal with the drum map manager. BFD3 can load various drum maps internally. Any change to the mapping will show up in Sonar.