"Send automatic 'we received your application' message" means that when the applicants submit their applications, they get an automatic email confirming it was successful. You can edit the sent message in "Your own status updates" section on the same settings page, and it will be sent right away after application submits with no additional approval from you.
"Send automatic status updates" suggests you good moments to update candidates and generates messages automatically. The first moment after an applicant has applied comes when you start to review them. You are then notified that an automatic status update is generated and will be sent in 10 minutes if you do nothing:
By clicking the notification or by scrolling down to "Timeline" you can see the generated message and edit/delete it. That is the only message now that will be generated based on your actions and sent without you clicking send button. If you don't want the VRA to generate these messages, turn the "Send automatic status updates" off.
Read more about the third checkbox and the applicant's ability to edit the application here.