Because many Title Updates have the same name they will overwrite each-other, meaning you cannot extract them all to the same folder. Yet when you inject a TU it will place it in the proper place, such that they do not interfere with each-other. I think the TUs should be extracted in a manner similar to which they are injected, that they should be organized into their proper place to prevent them overwriting each-other.
Horizon does not modify the file injecting or exacting. If you are exacting multiple game TUs you will need to either rename so there is no conflict or put them in different folders.