This extension solves that issue perfectly. Most of my system mail is now going through Mandrill. Some extensions, though, are built in a way that won't recognize this extension. But that's not a problem with CMandrill.
What began as an effort to avoid using my host's shared IP addresses for email has now turned into a new effort to use CMandrill and Mandrill for transactional emails. I feel like a kid in a candy shop.
I haven't seen any problems with SEO. Actually, it's improved SEO since client sites are resolving as Google, Bing, and Yahoo expect.
I tested out the extensions ability to send email as the parked domain - it worked really well. So well, though, that Akeeba Subscriptions was sending subscriber notifications from the parked domains - unrelated to the domain the user subscribed to. Had to leave those settings blank in Virtual Domains and just live with system emails generated by the installation's domain name.
I haven't experienced any system slowdown with it. Caching seems to work fine. Though, I did discontinue using jbetolo as it got a little confused how to cache info across the virtual domains. It worked, but a savvy visitor would see cached css and js from unrelated domain names. It looks like I could play with the settings more as the newer version of Virtual Domains provides more features that might work around it.
The extension also works really well with Akeeba Admin Tools in play. It was a concern how the two would get along and I have had no problems at all.
Brilliant work, Developers. Thank you.