"Players may not make post-production modification of discs which alter their original flight characteristics. This rule does not forbid inevitable wear and tear from usage during play or the moderate sanding of discs to smooth molding imperfections or scrape marks. Discs excessively sanded or painted with a material of detectable thickness are illegal."
From my take of the rule, I have interpreted it as being fine to flatten discs. When I am flattening a disc, it was either a roc, buzzz, or firebird, and I was trying to get them to fly like their original flight characteristics of the disc that I used to own that I wanted it to fly like. It is not my fault that the companies have terrible quality control and can not mold up their discs to be the same from run to run so this rule allows us to do that for them. Just my interpretation, I know most of you see it differently.
I disagree with your interpretation. The rule does not say change it so it flies like a disc you used to have. If I am seen taking a knife to cut off the flashing of a disc I can be called on it even though I was just trying to get the disc similar to my other disc and the flashing was going to wear off anyway.
If you want to flatten your discs, I no longer see a problem with it. It is not giving you an advantage and you are risking creating an inconsistent disc or even damaging your disc. I think it is illegal in the eyes of the PDGA, but if I took the same disc and tacoed it on my first throw I would try to use boiling water to restore it to it's factory condition. I would be doing the exact same procedure as someone making an illegal modification and mine is legal because I threw the disc just one time.
Aerobie tells you to bend the crap out of your discs before use to "tune them in". So where is the line where you have gone too far in modification?