Mr. Pogue offers no real answers to the question posed in his article. This is implicit in the (seemingly) purposefully confusing order given to the hypothetical list of photographic manipulations he offers; I would have placed burning and dodging in the darkroom higher up on the list (i.e. more innocuous), given the reality that burning and dodging is often a technique used to compensate for imperfections, not in the subject matter (i.e. objective reality), but in the inadequacy of the tools and materials of photography; my cheap enlarger causes light falloff at the edge of the frame; or my film exposure and developing methods can't adequately control or capture the scene's contrast range, for instance. These sorts of "manipulations" are merely techniques of process, intended to compensate for intrinsic inadequacies in tools and methods.
That is where I would "draw the line" (as Mr. Pogue urges us to do); it is, in my view, a question of faithfulness to the truth of the moment as perceived by the photographer, the principal distinction between photography and illustration being not so much of optical literalness as the technical details of the process rely on a 1:1 correspondence between an optical wavefront and a light-sensitive medium. Airbrush artists can achieve illustrative images of near photographic realism; but the distinction between airbrush illustration and photography goes back to the moment of image capture. Photography is always somehow reliant upon the techniques and materials of craft in order to remain photographic. It has always been a tenuous balance between an over-emphasis on tools and process and the abstracted final image, removed from the milieu of process.
When we talk of "oil painting" or "watercolor", it is understood that the genre is intimately involved with the physical materials and methods of certain, specific kinds of painting. Though we could simulate the visual technique of these methods using a Wacom tablet and Photoshop, it is commonly understood that they would no longer be oil or watercolor works. So it is with the distinction between photography and photo-illustration.
~Joe