It invalidates w1 of dyna-divergence, which gets little enough attention as it is. I'm not saying a whole lot of people go in and kill boss for medals, but it's an extra prize for doing a quick in-and-out boss for someone. People farming W1 creates shards at a cheaper rate than medals and provides a secondary market.
Is it really that much better to have a handful of RMT sitting on 50,000 medals and providing all of them at 300k/pop so you can upgrade easily? Why not make everything worth very little gil? For that matter, why not make a NPC that lets you select which r/ex pieces you'd like and get them for free?