I have a couple of accounts that I don't need to access too often, so i have set each account pref (advanced tab) to not check for mail automatically by unchecking "include when automatically checking for new mail"

I don't know about Mountain Lion, but I found nothing in Mail preferences in either Lion or Tiger to tweak those kinds of settings.

I also searched the plist files and found nothing there. But, I was a little bit hesitant to experiment too much. If you find something, please share. Usually, the plist file is Library > Preferences > com.apple.mail.plist. From what I see on the internet, it should be the same for Mountain Lion. Your library folder may be hidden. In Finder, pressing shift-command-g and typing "/Library/Preferences" and pressing enter might get you to the preferences folder.

I think he'd want to go to ~/Library/Preferences/ for his own preferences.

All those sort of deep mail settings are either hard coded in app or Apple will never publish the plist keys but in Mountain Lion the Account info is stored in ~/Library/Mail/V2/MailData/Accounts.plist

Sparrow continues to work fine, even though it won't get updates.

Quite right. I neglected to add the tilde. /Library/Preferences doesn't even contain a plist file for Mail.