Domain Mapping & Jetpack Connection

I am having an issue with Jetpack connecting with multi-sites using the domain mapping plugin.

Jetpack connects to the site url with the .com but since the homeurl and siteurl are still the sub-domain version it now causes an error conflict with Jetpack.

Do I need to have the domain mapping plugin update and run off the .com url instead of sub-domain url for Jetpack to work correctly? I'm guessing the issue is that the domain mapping plugin masks the domain with a .com but the sub-domain is still active as the homeurl and siteurl in the settings.