Migrating from MBA 2013 to Mac Mini Mid 2011 using Carbon Copy Cloner
My experience with Carbon Copy Cloner, which I use for daily backups of my external drives and for monthly checksum backups, is that, yes, it will copy anything that you do not tell it to specifically exclude. 

I'm wondering, however, if there is not a more simple way to do this; did you, by any chance, download the 'extras' directly from Apple, as opposed to from the Mac App Store, as a .pkg that you might have retained and, so, could simply reinstall? Many people had problems downloading the extras in the traditional manner and Apple made all (?) (most, at any rate) of those 'pro packs' available as a direct download from their site. The link I have for that download is:
http://audiocontentdownload.apple.com/lp10_ms3_content_2013/ProAudioCoreContent10.pkg