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I talked to @nelsonmc about this particular issue and it seems that the way this setting is working is to build a list of files to sync rather than what to sync. If you were to clear the table in the database that keeps record of all files needed to be synced and tried this process again you should only get the plugin files.
It seems that when I check the "Plugin Files" box for uploading, theme files are uploaded first when the theme box was not even checked.
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