In the Autostart section in the System Settings, You can't select multiple entries to then apply "autostart only in plasma" from the Advanced button. You need to go trough every single autostart entry and change the checkbox. I feel it should be possible to SHIFT or CTRL select multiple lines here
If we did this, then every other change you could make in the Properties dialog would be applied to all selected entries, and almost all of those potential changes don't make sense to apply to more than one entry. So I don't think we'll be doing this, sorry. But thanks for the idea anyway!