I would like to suggest a context-related Ctrl+S behaviour.
When I edit something in the attribute table, I would like to be able to save my field changes with Ctrl+S.
There should be a context-related behaviour depending on which panel is focused. If someone is editing features in the attribute table, I bet with you, most of the user wants to save these changes.
To avoid unwanted changes, a confirmation dialog could be shown asking if the user wants to save the project or the edited data. (Add a checkbox, so the user can decide if they want to confirm always or the context-related behaviour by default.)