The full package works the same, it just excludes some nonessential files for upgrades, files which some FTP programs might use to overwrite parts of your installation. In particular, the /data and /internal_data directories are very important as they contain all of your avatars and attachments and you don't want to possibly overwrite them which is why they are excluded from the upgrade package. The usual and expected behavior is that the FTP client does a "merge" overwriting only those files (not directories) which exist in both places, but not all FTP clients behave as expected and some can actually be configured to overwrite entire directories.
edit - I have also seen FTP clients which change directory permissions despite not overwriting the entire directory. That can also be a problem for /data and /internal_data because those directories need to be writable.