I was wondering if it would be possible to add design notes to entities in the project's navigator. Perhaps a note icon to the left of it and when the site is transferred they can be transferred with the notes attached. When the designer is happy with the project there should be a button where these notes can be removed.
I am afraid this sounds somewhat in a bloatware directon... I mean this is already out of the main focus of Webflow as a site building tool. Maybe you could use an application like http://notableapp.com instead?
If you use the Vivaldi browser, they allow for you to write notes on the side in the browser. Maybe this is the right solution for you.