Has there been some problem with the current system in which, if you want to travel to a country requiring proof of vaccination that you go pay for that, get it done and show them the piece of paper?

How the fuck does the El Salvador customs and border patrol know if your Shopper's Drug Mart covid certificate is valid? Foreign governments are going to want Canadian government certificates. They're not going to accept a scrap of paper from some random drug store or whatever. It's the exact same reason you can't buy a regular passport at Shopper's Drug Mart.