My experience was that there was a difference in how attrites were treated. (This doesn't necessarily mean that they were given preference in their follow-on orders, but there did seem to be a hierarchy in how they were treated on a personal level, and, at times, on how much the command was willing to go to bat for them.) NPQ's were generally treated the best (except the guy who got NPQ'd after going down to NAMI in an attempt to get anthroed out of Prowlers), flight attrites treatment was generally based on their attitude about the situation, and DOR's were definitely treated worse than the others (in some cases, instructors would completely ignore them).
There is one significant difference in being NPQ'd vs. flight attrite. The Regs (for all services) state that you cannot apply for a pilot slot if you have been performance attrited from any military flight program. There may have been exceptions to this, but it would be a lot easier for an NPQ to get back into military aviation (assuming the medical condition can be fixed) than a flight attrite.
While at Meridian, I saw this happen three times. A person was NPQ'd, but rather than giving them follow-on orders, the Command stashed them while trying to help them get over a medical condition, and then helped them get the necessary waiver. In each case, the Stud was stashed for over a year. Two of the three got their waivers and are now winged. Can anyone guess who the third was?