You do realize that the article is telling people that those brutal, enter your resume bit-by-bit within our especially tedious, custom format, online applications are a waste of time, don’t you?
It is well suggesting that finding the hiring executive and approaching him/her is often better than going through that anonymous HR meat grinder.
And that is often, though not always, true. I don’t think anyone can disagree with your specific suggestions re: a cover letter, however, either.
Sure if you don't know what you're doing. Most of the sites have an option to upload a resume. Or you can upload it and it will parse out what you need. Or absolute worst case, you have to cut and paste into separate fields. IF one takes time to develop their computer skills these are a piece of cake to navigate. I know...I've done it hundreds of times!