how does set_post_thumbnail_size() make sense?

Technically, you don’t have to call set_post_thumbnail_size() at all if you want to use one of the predefined sizes (on a personal site, you’ll change these at Dashboard > Settings > Media); you can just pass the argument directly to the_post_thumbnail():

<?php the_post_thumbnail( 'large' ); ?>

If you’re developing a theme for distribution, where you can’t count on being able to set the image sizes, you call set_post_thumbnail_size() to explicitly set the pixel dimensions of the post thumbnail, if you need a specific size to work with the design.

Yeah I know all that, but what when I don′t want my upload folder cluttered with image sizes I don′t need in my theme?

You could set all the sizes to be 0, which would suppress the automatic resizing for all newly-uploaded images. You’d also have to make sure your theme and any plugins don’t register any custom image sizes.

You could then manually remove all the automatically-generated resized images from wp-content/uploads, but you’d have to carefully check all previous posts and pages because the image links are hardcoded to the specific size when you originally wrote the post/page.