You are correct. Removing the tweaks is as easy as unchecking the boxes next to the tweak.
The tweaks themselves should not have installed anything on your phone other than perhaps a picture or two for the boot logos, etc. The downloads you saw were most likely the WebOS Doctor download which can be used with (or from) Quick Install to reset your phone. There are "mods" and/or patches that can be added to your phone which do require a file to be copied across. These should also be removed prior to performing any updates.