Well, I have 2,693 published entries and 23 drafts, so it doesn’t quite add up to 3000. But I confirmed the first and last posts are in the file — what could account for the discrepancy?
File attachments (like picture uploads). Those take up a Post as well. So do Pages. And starting with version 2.6, so will Post Revisions.
Can it really optimize by more than twice the size?
Yes. Quite easily, in point of fact. Databases are different than normal file systems, the same rules don’t apply. And when you do an upgrade, with something that alters the table, then the database will be optimized in that process. This is normal, pay it no mind.