Ok, so after looking through the code I came up with a solution. As stated above the autoversioning stated on the wiki is not enough to automatically version files of the same name upon upload.
The multipart mime submissions for file uploads has an "overwrite" parameter which, if set to true, will automatically version files of the same name (if the file has the versionable aspect).
The default behavior is to have "overwrite" set to false. (I think this behaviour may have changed from a previous version of alfresco)
I could not find a global paramter to modify this parameter, so I modified the client side JS files to turn this on by default.
I modified the "overwrite: false," to "overwrite: true," in the following files:
dnd-upload.js dnd-upload-min.js file-upload.js file-upload-min.js html-upload.js html-upload-min.js
if there is a better way of doing this someone please let me know.
If this is the easiest way to accomplish the task. It may be appropriate to have a feature request to expose this behavior in alfresco-global.properties, or somewhere else more excessible. I doubt I am the only one who desired this type of behavior.