Yes. As I said above, the system is set up to deduct it in a specific order:
POL
AA
ALA
ILA is the whole balance of POL+AA+ALA - by ticking the box, you are merely saying "take it out of my normal balance".
The only way to get round it if you have already returned is for your POL to be removed by HR, then the leave pass actioned to JPA, then the POL to be re-instated. It would take a clerk around 30 mins to get all that done, plus time spent the next day checking its all worked correctly.
How do I know? I've done it a few times in the past for my Sqn guys (yes, many of whom were TG1 and didn't slag off TG17)
Good luck in finding someone who will go through all that for you when they have no service reason to do it!