I'm not familiar with that plugin, but Jetpack Subscription emails are actually sent from our Jetpack servers at WordPress.com. There is not currently any way to customize them.
We're working on adding a few more options to customize the text, but we don't currently have any plans for customizing the style/look/feel.
Also, the Jetpack Comments feature isn't currently compatible with other subscriptions plugins, so to use another subscriptions plugin, not only would you have to turn off the Jetpack Subscriptions feature, you would also need to turn off the Jetpack Comments feature. We'd like to make Jetpack Comments more extensible, but it's a little limited at the moment.
To turn off a Jetpack feature:
1. Go to your admin → Jetpack
2. Click the "Learn More" button on the feature you want to turn off.
3. A "Deactivate" button will appear next to that "Learn More" button.
4. Click the "Deactivate" button.
Sorry for the hassle :(