Does the cheap/free pre-issuance submission really matter when you have to spend thousands of dollars on a reexamination fee whether or not the patent gets invalidated or modified in the end?

I get that this is to help cover the USPTO's reexamination costs. But whatever the reason, it's still really expensive to call bullshit. And as the grandparent comment laments, this is a real shame given the low quality of many patents that are granted.

In this case a third party did the job the USPTO should have done when the patent was first filed by actually reading the patents citations and finding that the new patent wasn't a novel innovation on the cited patent.

Wouldn't it be nice if the USPTO paid the third party his $6000 back if they determine that he's right the patent should have never been granted in the first place?

Ah, that makes more sense. You had your chance, but we granted it.