In this lecture video at 6:00 when Ben is explaining why not to extrude both upper holes at once I found out that is actually far better to do it that way without any problems afterwards as Ben went through in his video after his extrusion where bottoms of holes collided with each other. See my images below…
After extrusion, nicely lined up next to each other.
Here, you can see all faces being selected at once.
And here, extrusion itself where you can see both holes going straight in along Z axis, not crossing each other.