With the added context of
this post by the OP, perhaps the desired answer is of a more technical nature.
Gary is the only one who can provide answers with certainty, but from as far as I'm aware, those buttons merely instruct VoiceAttack to ignore any input it detects(and to allow any keypresses that would otherwise be prevented from passing through to another application to do so).
This is supported by the fact that state tokens keep working for both of them.
Setting up a joystick will mean VoiceAttack polls that device(I.E. it asks for information about the buttons and axes) at the interval set in the "Joystick Options" window.
In theory that shouldn't interfere with other applications, as the API that is used should allow multiple applications to access a given device at once.