I think its problem that we should worry about if we ever make it to the latter stages of selection but I too will hopefully have my PPL before the course start date, and I'm not intending on re-doing it! Once you have the license, you have the license, surely! Common sense will hopefully prevail. Some extra hours will be nice though.
It does state on the FTE website (see previous post for link) that students with a PPL will be entitled to a discount on the course price after a positive checkout with the CFI. Every little helps! Regards your atlp's I have no idea.
I'm purely speculating of course so could be way out. Like I say I'm more worried about actually getting to phase 3 over anything else!