The difference is that NEW wheels have the back pad "shaved" (via lathe or mill) BEFORE the lug holes are drilled. This region of the wheel must have the correct cross-section (especially in a cast, rather than forged wheel) so the lug seat area has the appropriate strength.
If the lug holes are already drilled, 3mm (about 1/8") is all that can be safely shaved.
Otherwise, as mentioned above, the lug holes should be "filled and drilled" , then the backpad milled, then the PCD holes re-drilled... but I would NOT recommend this. Some shops say they can safely do this, but it is impossible to predict how the welding will affect the temper of the aluminum.
If you're having clearance issues, an offset change of 3mm may not fix your problem. How about using a narrower tire to make up the clearance difference?
A lot of the 'JDM VIP' guys do this on big-bodied cars... stretch the tires a bit, perhaps a 235/40-17...
For comparison, my MKI has 18x9 +38 on the rear- sticks out past the fender just a hair. I will stretch the fenders a little before repainting the car, but the 235/30-18 tire actually clears the fender!