Library/mail folder storage very large

Background:  Using an IMAP account, I switched from Outlook Express (under VM Ware on same MacBook) to Apple Mail because I wanted better archive control (generic .mbox versus proprietary MS .dbx archive format) and to get past the OE 2gb message file limitation.  As an Attorney, I download every message and attachment to local drive and backup and archive.
Q1:  Gmail says I am using 6.1gb out of 7.6gb with 8,146 "All Mail" messages.  Apple Mail "Account Info" says I am using 6.1gb out of 7.4gb (close enough), BUT counts 14,392 messages at the same time.  Why the difference in message counts?
Q2:  "Get Info" for Users/.../library/Mail reports 13.24 gb, over DOUBLE the actual storage for all the messages and attachments.  Why the increased hard drive space?
Q3:  Mail Preferences "Accounts/Advanced" has a setting for "Compact mailboxes automatically" which is selected and greyed out so that I cannot change it.  In theory this sounds good, BUT I am finding that Apple's documentation for Mail is very poor and imprecise, and I do not know what Apple "compact" actually does.  In other email programs, "compact" can actually strip the message and leave only the tracking and Subject data, which I do not want to do.
What is actually happening in "compact", and why can't I changed it?
NOTE:  when I setup Apple Mail, I was not sure exactly what some of the Preferences should be to get the same end result as with Outlook Express.  I told Mail to sync with Gmail and let it download ALL messages and attachments, which I think it did.  When I noticed the message count discrepency, I checked to see if anything was missing, but found not evidence of loss.  I did a quick lookup on "Rebuild" and gave it a try.  It took all night at 3megs DSL download speed and it appears from the data storage size that everything is downloaded, even thought the message counts differ.  I do not know if "Rebuild" first makes a "Copy" and then duplicates the message store, and then deletes the "Copy" as cleanup, OR if it duplicates the existing data files.  I have not found any duplication in the files or in the messages, but this may explain the doubling from 6.1gb to 13.24gb.  Any ideas what is happening?

shonamelissa wrote:
Could you please tell me if MailAccounts.plist will hold all my IMAP messages if I back it up?
No, it will not, it's only a 2-byte file, almost nothing. That file only contains settings about your mail accounts, not the contents of the accounts.
Your mail messages are in the Library/Mail folder. If you "keep copies of messages for offline viewing" with IMAP, complete messages and attachments will be stored in that Mail folder. You can tell by looking at how the file size of that folder grows and grows, and also by digging into that folder and looking inside the account subfolders. Messages are stored as RTF files that you can open in TextEdit or Word, so that is another way to verify that the messages are indeed being stored locally as well as on the server.
To completely back up your Mail messages and configuration, you should back up the Mail folder with all your messages (after making sure you are keeping local copies), MailAccounts.plist for your account prefs, and com.apple.mail.plist for other preferences.
I don't really worry about it because both my Time Machine and clone backups are of the entire Mac. Mail is naturally included.
I think the tech note you were reading might be assuming that "Keep Copies of Messages..." is off, because that's the default. But if you turn it on, then sure you can back up the local copies of messages that are there. After you give Mail a little time to cache them all.

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