Yes you can use Relative Positions with Export Kit Pro, and it will do so. What happens is the folder will become “position: relative” and the layer contents of the folder will be “absolute” within.

Note that Photoshop is a position based (x,y,z) environment, while HTML is a screen based (flood fill) environment – we aim to have your output as similar to your Photoshop doc as possible.

Take a look at Photoshop vs. Environment Rendering and export the example PSD in each environment to see the difference.