How does it work?
Checking this setting gives you the "full" automation experience. It allows your quotes/invoices to automatically move around between different statuses (such as a quote converting to an invoice, or an invoice going from "unpaid" to "paid") upon entering the correct trigger stage. To enable it, check the box and click Save Changes at the bottom of the page.
Why would you potentially not want to check this setting?
You may want to leave this setting unchecked if you'd like to be able to create a quote or an invoice in whatever CRM stage, but you don't want it to move around automatically. For example, if you want to create an invoice from scratch in its proper stage, and you want it to stay there until you move it manually, then you would want to keep the pipeline turned o, but have this setting unchecked.