Rsync different behavior when syncing folders HDD-HDD or HDD-Ext HD

You want bi-directional sync. Take a look at unison, which does this: http://www.cis.upenn.edu/~bcpierce/unison/

For example, on Debian/Ubuntu:

$ sudo apt-get install unison
$ unison MAC/ LINUX/

If you have trouble with permissions (example ext4 -> FAT):

$ unison -perms 0 vlc-2.2.0/ /media/sf_vlc/vlc
Contacting server...
Looking for changes
Reconciling changes

vlc-2.2.0      vlc                
new dir  ---->            /  [f] 

Proceed with propagating updates? [] y
Propagating updates

You can use a leading / to match only in the root of the transfer. Try this:

rsync -avCz --delete-before --progress --exclude=/test/ /tmp/codebase/ .

Here is the man page snippet for the leading /:

if the pattern starts with a / then it is anchored to a particular spot in the hierarchy of files, otherwise it is matched against the end of the pathname. This is similar to a leading ^ in regular expressions. Thus "/foo" would match a name of "foo" at either the "root of the transfer" (for a global rule) or in the merge-file’s directory (for a per-directory rule). An unqualified "foo" would match a name of "foo" anywhere in the tree because the algorithm is applied recursively from the top down; it behaves as if each path component gets a turn at being the end of the filename. Even the unanchored "sub/foo" would match at any point in the hierarchy where a "foo" was found within a directory named "sub".

And for the trailing /:

if the pattern ends with a / then it will only match a directory, not a regular file, symlink, or device.

Update

I am guessing from you comments that you are also looking for the --delete-excluded option.