Thank you for your feedback!
You can already edit the list of files, folders and registry data before the uninstallation starts, so I don't see the need to add any checkboxes there. That would just add complexity. If you don't want some path to be removed, just remove it from the list.
About your idea of removing the startup script, I think that is a good idea! But I think it should be an additional option, instead of coupling it with the automatic reboot option as you suggest. I will add an option about this for the next version.
