I don't think the system is flawed, I think you're just wanting it to be something that it is not. It is a tool that has been developed to track relative performance over a period of time because not all courses are the same difficulty. Not all courses in the same "difficulty" are the same difficulty. I've played Red (Rec) courses that are harder than nearby Blue (Advanced) courses because par is relative to whoever the course designer is. In the system there is some inherent built in variance, so courses are typically "graded" on a variety of factors and not strictly the rating. And the ranges for determining difficulty of a course is usually within a set range, and these ranges often overlap.
The other thing to note, is that ratings allow for things such as weather to be taken into consideration when judging the relative performance on a given round. If someone shoots -6 on a sunny, blue sky, low wind day - they are probably not going to have a round rating as high as they would shooting a -6 on the same course on a particularly windy or rainy day.
As with any statistic the PDGA Rating system should be viewed as a guideline, which is does a great job at performing its given function. And as with any statistic it is not perfect and therefore technically possibly to be "abused", depending on your definition of abused. There of course would be little benefit to abuse the system other than personal ego inflation. With enough rounds played, the system works itself out.
While not a perfect example, quarterbacks in Football are often judged by their completion percentage, but that statistic does not factor in how many of their passes are dropped. NBA players are often judged by their free throw percentages, but people rarely look at how many free throws players attempt per game to realize the difference between an abysmal 70% free throw percentage is only about 1.2 points different for most players compared to an upper end 86% percentage. In golf Greens in Regulation can be skewed because of how they are often shaped and sometimes it's better to be off the green on the correct side then on the green on the wrong side.