This is intentional. Viewport height only changes the simulated browser height in the designer, so you can see how your layout responds to a taller or shorter browser window. It doesn’t change the page’s saved layout, so the project stays unmodified.
Actual layout changes, such as Row Span or Fill remaining, are saved and undoable as usual.
I can see how the label could be misleading. Preview viewport height would make its purpose clearer.