Some cans that are designed for lowmount, like Sato, are considerably longer than the high mount version.* By as much as 100mm's. Not to mention the issue of making sure the canister inlet matches the midpipe outlet. Although there are many adapters available to make some of the more popular brands mate up. You'll need to do your due diligence.
*The longer the canister, the more tolerable the noise level, and the better it is at getting the noise away from you and your bike as you're riding. My Sato lowmounts are about 450mm's long. I believe the Sato high mount or bonzai is about 350mm's long. Someone please correct me If I'm wrong.