I don't believe there was a difference until somebody saw the opportunity to make some extra bucks and "developed" a muzzleloader specific 209 primer. Enter Kleenbore by Remington and others. Here is a good article by Randy Wakeman on the issue.

http://www.chuckhawks.com/winchester_777_primers.htm

I just purchased a can of Blackhorn 209 at bass pro shops in Sevierville Tennessee.
On the back label above the loading data it states use standard 209 shotshell primers.
Do not use 209 muzzleloader primers. I know it takes a hotter primer for BH 209 so Are
these hotter as well.

WV Mountaineer

From the Knight Rifles website's FAQ section:

Which primer is hotter?
The 209 shotgun primer provides the most gas pressure.

Vince