I found this thread because I was looking for the same thing. We definitely need a 'ginput' function that works within a UIFigure.
However, I did find a workaround: invoke a new 'normal' matlab figure with 'figure' (e.g. MyFigure = figure;) plot on that figure any plots/graphics that you have plotted on your UIFigure (any relevant graphics that you need on there to be able to click relative to). Note, use the traditional plot() command, rather than the plot(app.UIFigure, ) command. Then use the ginput function with that figure. (e.g. MyPoints = ginput;) then delete the figure, and use the recorded values as desired. (e.g. delete(MyFigure); )
This actually worked well for me, as the 'pop-up' figure is larger than my UIFigure, allowing for more accurate mouse clicking.
Hope that helps. Cheers, Hugh.