Its submission includes the view that the uniformity measure, which it felt would hamper the use of covermounts, should be changed.
Royal Mail proposed that items 10mm thick should be classified as packages rather than large letters, with a tolerance of 2mm.
The PPA argues that tolerance should be 5mm enabling publishers to "accommodate product variations without risk of incurring a cost penalty and to budget more effectively when planning advertising and promotional activity".
A case was also made for Postcomm to press for more disclosure of Royal Mail's cost structure.
The PPA is urging Postcomm to ensure an 18 month timeframe for adjustment if size-based pricing goes ahead.
Postcomm will use its responses to assess Royal Mail's plans and a second consultation document is expected in the autumn.
Royal Mail has unveiled a 25% discount for weekly magazines. The promotion is aimed at publications that have less than "5% actively purchased UK single copy subscription sales".
Story by Philip Chadwick