May I use width and height CSS properties on images?
What I understand is, it is suggesting opposite to what you are interpreting. 

Lets take a look again. 


  Never apply widths or heights except to elements that natively have these properties (e.g. images).


So, it is saying that, you can apply the height and width to image freely as the Height and Width are the default property of images. This you can understand as all images has some width and some height. So they are intrinsic property of image.

Now, lets take other proof, why you can apply Height and Width to image. If you see the Drupal's core feature, 
Image Style at Admin/Config/Media/Image style, there you can specifiy as many image style as you want with different Width and Height.


  


Hence this feature allowing the facility to  change the dimensions of same image with different Image styles - AND how this is happening, simply by changing the height and width, So this is the core feature.

Hence, image comes in the category of except in your highlighter following statement.  


  Never apply widths or heights except to elements that natively have these properties (e.g. images).


So, you can freely use width and height to Images.