How do I abort a data upload in Workbench without having to go into setup in Salesforce and abort it there?
There isn't a way, as far as I can tell.
How can I modify the batch size while it's uploading/updating lists of records from a csv?
The batch size is already determined when you start the process. This is a feature/limitation of the underlying API. The workbench tries to keep the files of the correct size so as to not trip over any batch size limits.
How do I turn off the auto-mapping of my csv from the file I upload?
The workbench is not a "production-quality" tool that you should rely on. It has limited support and limited functionality. This is noted in the Terms of Service.
If you want to try to make it better, you could always clone the repo, add features, and even do a pull request if you want to have those features. Or you could host it yourself.