He doesn't actually draw with the selection, he stretches the selected area higher. The layer contains only 2 colored pixels which are stretched higher. He operates with keyboard shortcuts to be fast.
An example in GIMP:
The image is 50 x 50 pixels. It has 2 layers. The bottom layer contains large blue and red dots. The top layer has only 2 single pixel red dots above the big blue dot.
The small red dots are selected with the rectangular selection tool:
The content of the selected area is stretched higher with the scale tool. GIMP leaves the result floating, so you can still decide do you want to continue the scaling, anchor it to the top layer where you started or do you want a totally new layer:
To get pixel perfect result with no antialias blur you must select in the scaling tool options Interpolation = None.