Hi Ben,
I did try plugging in after Pro Tools opens. I do remember it working at least once. It wasn't consistent though, especially if I was changing sessions.
It seems inconvenient to me to have to unplug hardware from the computer every time I want to use it with the software. With my solution above I can accomplish essentially the same thing with two mouse clicks and so far it's working consistently.
Until someone can tell how to disable the MidiOut port for Spark in Pro Tools, or a way to prevent Pro Tools from seeing the port, I can't think of a better way to do this. Ability to disable the ports in Pro Tools, like can be done in Reaper, would be ideal.