First off, this is about Stacks which I didn’t realize.
Every Stack, just like a Layer Instrument, has its own channel in the mixer. While a Stack is a complete submixer on its own, you can send from the mixer channel to Group (Fx) channels, use the “e” button on the mixer channel to expand). Maybe that helps. Also you can copy/paste Stacks and drag/drop into and out of the Media Bay to the right.
As said you can do that with the Stack Channels (in the mixer), but not within Stacks, those are closed sub,ixers.
When the items turns yellow it should learn whatever you send. Make sure your MIDI input port is assigned in the Devices/Connections setting.
You may be comparing apples to onions, because it depends so much on what is going on in addition. If you run a full loaded project in DAW a and just testing video in DAW b, results may be quite different. To compare, create just one video track and remove all global fx etc.
Not sure if it helps to send a file, if you have a short one we’re happy to test it.
Sync is planned (MTC, but no LTC; we may send LTC in the PRO version later though).