You are correct, the setting that you see in X > Theme Options > Buttons work only for the Classic Button elements. The new V2 button element has its own styling. For more information please read the article below:
Now, there is a new feature called the Template Manager. The way it works is that you add a Button element and using the options given to you by that element you can make the button flat. Then you can make a template of that button and set that template to be the default view of the button element.
After that, whenever you add a new button element you will have that flat style. Please check the article below for more information about the case:
The cool thing about the method above is that you can do this for every none classic, V2 elements.
Additionally, please make sure that you will enable the Advanced Mode if you want to have a complete control over the options of the elements. Read this changelog to know more about the advanced and simple mode.