I recently did this course and it’s true, following the process shown in the video things will become uneven. Jonathan attempts to correct the issue and then proceeds with the rest of the video (around 15:20).
That said, I think this video is more about getting comfortable with the tools and navigating Blender in a project-based way rather than teaching good modeling practice. That comes later. If I remember correctly he gets into that aspect of proper modeling in the Pothead course.