I'm not sure that i completely understand your setup, given the last sentence, but here goes:
Alt.Binz needs the small par2 to do any verifying and autounpausing for repair (of just the par2s needed) and for unraring - you should always allow this to be downloaded (see Setup).
Scripts will always run when the configured cycle is complete. So if you disable par2 checking & repair in setup, it will run when download is complete (very unwise though).