Bottom line is: it doesn't matter.
Rank the programs in the order that YOU WANT TO GO TO THEM.
Let's say you only interviewed at two programs. Program A is really great, but they have ranked you at the absolute bottom of their list. Program B is not really that great, but you'd be willing to go there. They have ranked you #1 on their list.
You should rank A first, and B second. The match will try to place you in A. Perhaps you'll get lucky and get a spot. Perhaps not. If not, you'll get a spot at B. YOU CAN'T LOSE YOUR SPOT AT B BECAUSE YOU RANKED IT #2. (Well, the only way you "lose" your spot at B is by getting a spot at A).
So, yes, if you get these types of emails they might make you feel all warm and fuzzy. And, it might help you have less nightmares between now and match day. But honestly, it should not change the order you rank programs (unless being "really desired" by the PD is one of the criteria you are considering for programs, which I guess might have some weight but shouldn't sway you too much)