Yes. In Pixel's code there are four death events for ballos: #0500 (I think) is first form's death sequence and animates the special boss of the map, and starts the second form. When the second form is defeated #1000 is called, a flag is set and animates the special boss so it becomes the third form. When it dies it calls #1000 again, however a <FLJ changes the event to #1001, which starts the fourth form (and I believe another flag is set). After this the same thing happens IIRC: it FLJ's to #1002, which starts the fourth form death sequence and the final cutscene.
What you need to do is look for the event with the BOA/ANP for whatever form you want (whatever event the h/v trigger triggers for first, #0500 for second, #1000 for third and #1001 for fourth) and then use the boss' death event (#0500 for first form or #1000 for others) and paste the death sequence of the form you want in that event.
For example if I only wanted Ballos' fourth form, then I would start it immediately using the <BOA from #1001, then change #1000 so that the death sequence code for the fourth form (event #1002) is contained in that event.
However, no matter what form you use (except for the first), I recommend you always use the fourth form's death event, because that makes it explode. Otherwise it would just stay there.