So in the process of experimenting with CAS parts, I discovered that a good amount of the packages I've downloaded are considerably oversized.

That is, exporting the vital textures from an object in the CTU, deleting all of the larger images in s3pe, and reapplying the textures again in CTU seems to replace a ~12mb package with a 300kb version, which seems to run just as well.

So what is mucking up the files so much? Are there any tools out there for automating this sort of cleaning? Or a better process for doing it by hand?

Or am I missing something?

Those packages contain prolly uncompressed files.
TSRW has the option to save the files as package, but they are uncompressed giving you a huge download.(not sure if they fixed this with their latest version tho)
Also files(in the package) that have been edited with Postal lose their compression, i always use S3PE to fix these.
When you open a package with S3PE you can right click the file and compress it.

Et voilà.

Thank you, Base.

your welcome