It seems like a weird bug, but this code makes it work. If you add drawnow in startupFcn, the FontSize can be changed, but make sure that the font size is different from the number in the component browser, otherwise it won't be changed.
Credits to TMW Customer Service
app.EditFieldLabel.Text= '\[ x^n + y^n = z^n \]';
app.EditFieldLabel.FontSize = 25;