Anyone know how to package apks? (or .mtz themes, for that matter)?


Not completely right.
.mtz are ZIP-Containers - in WinRAR you have to say: 'only store' - because it isn't compressed and not so much work for the phone to access the files inside.
The same goes for .apk and .jar.
Only simple .zip-containers. Rename them to .zip, and do whatever you want. ;)