The nice features in the Query Designer that allow you to drag and drop tables into the query, drag columns around to complete joins, etc. means the UI takes control of the query text so it can present what was designed in the visual areas of the designer in the query text pane. Not much you can do about that. And unfortunately redgate SQL Prompt doesn't work its magic in the Query Designer.

If you want ultimate control over your query formatting use the Query Window by right-clicking on the View, selecting Script View As, then Alter, then New Query window. From there you will be working with the actual view-definition, but of course only in its textual form. Altering the view in a Query Window will maintain its formatting whereas working with it in the Query Designer will not.