At first I didn't really understand how it was misguided, but the more I look at it, the more it seems...odd.
I mean, it has it interests at heart but I have seen kids play with puppets while their parents or any other adults interacted with them and greeting the puppet as a person. It doesn't need to be in an instruction manual, it's should be just a natural reaction. If a child asks you to say hello to their puppet, you better say hello!
I guess the manual's point is to get kids to encourage puppeteering? But, to be honest, I can think of better ways to do so without a manual. In fact, I HAVE taught kids how to handle puppets. (Admittedly with another adult who knew more about kids than I do, but still)
Perhaps when you give a puppet to a child that young, you have to teach them to not get the face dirty and to not play too rough with it and then let them do whatever. It's a little different with a 12-year-old who wants to do it as a hobby or a serious career choice, but that's something else entirely.
And, yes, good point! If you are going to make a manual about puppets for kids aged 2-4, why only use he/him/himself? Does the author really consider female hands to be too weak to stick up a bit of felt? Surely whoever made this would want a general audience regardless of gender, right? Right?