I can see three reasons for this:
- Packages in the base image or installed via the application manager while doing a SSU are more compressed than the rest of files. (Same reason upgrading Maemo with apt-get instead of H-A-M uses slightly more space after the procedure). This however only accounts for a little %.
- UBIFS might have troubles calculating free space until a GC run or a reboot. JFFS2 at least had.
- There's a browserd process that keeps the microb files in use. This means that even if you unlink (delete) them, they will be kept in the disk as long as the browserd process keeps using them. Even if you overwrite the file names with another set of files, the original file contents will remain on disk until browserd dies (and of course, browserd died when you rebooted).