Is there a way to override the stock keystrokes fired into a DAW when set to a generic Target App?

Yes, create a file named ‘keysOverride.txt’ in your settings folder at MyDocuments/BaseHead 5.x

Once you create this you will see a yellow label with the word ‘overridden’ next to the Target App selection combo box telling you that it’s engaged.

Inside this file your can place 4 key commands that you want to fire comma separated.