Hi,
I have used Bars & Pipes a lot with MTC and MIDI-Clock. Even know a lot about the quirks of this. I used to slave Bars & Pipes to an external Yamaha MD8 digital Multitracker with MTC. You can even have Bars & Pipes sent MIDI Machine control out to the digital multitracker so you can use Bars & Pipes transport controls to start/stop the external multitracker, but then have the multitracker send the timing code.
I have also used Bars & Pipes to control a slaved drum machine / external sequencer.
I also use a MIDI solutions 4in to 1out MIDI merge box to feed my Amiga's MIDI port.
So, am I understanding your problem correctly? You want to slave B&P to your multitracker, but then also use the multitracker' MTC to sync some other outboard gear?
I would be very surprised if B&P will not pass-through the MTC code it received to the Amiga's MIDI out port so your other devices can use it.
If not, a hardware solution would be to put a MIDI splitter on the MIDI out port of the device generating MTC (your multitracker). Feed one output to the Amiga, another output from the splitter to your outboard gear that needs the MTC signal.
As for the note off problem with your MOTU gear, there is a small plugin tool for Bars & Pipes that will make sure a NOTE OFF signal is generated for every NOTE ON signal it receives. Put this on the end of the pipeline of the track. This might solve your problem.