Introducing Exchange Online Tenant Outbound Email Limits

BoBeB is right that Journaled messages (using the EXO journaling method) are entirely exempt. For regular messages to external recipients if it routes out to Mimecast then back into EXO for delivery to the Internet / the external recipients, then yes, at this time it will get double-counted to help protect against spoofing mid-journey. Only true for external recipients - this limit doesn't track against internal recipients at all. We're looking for a way to both prevent spoof and not double-count and hope to update this later this year. 

FWIW, here's the FAQ that's trying to answer that question - I realize it might be a bit confusing as it singles out signature service and on-prem; but it's just an example of the general scenario of sending out to the 3rd party service -> back in to EXO -> out again to external recipient.

If I send a message to an external recipient but it routes out to a signature service or on-premises for processing, then comes back into Exchange Online to be sent out to the external recipient, will that get counted twice?
To reduce the risk of bad actors spoofing on-premises systems to send spam, we are currently counting these messages more than once. Our telemetry shows only a relatively small number of tenants are currently exceeding their quota, so it’s highly unlikely this will be an issue for your tenant. That said, we’re investigating alternative ways to prevent this type of spoofing that won’t double-count such messages.