First, I don't get how putting the tube in the mouth is any different than using the mask -- the mask is merely delivery method -- it doesn't mean she gets less of the medicine in her lungs. Besides, if you put the tube in her mouth, the medicine is bound to end up more in her mouth (and tastes bad) than in her lungs where it does its work. I would ABSOLUTELY ask the pediatrician about that. It makes NO sense.
Second, I would go ahead and use the mask because, if she's fighting the tube put in her mouth, she's getting a lot less of the medicine than if you just use the nebulizer the way it was intended.
How in the world does anyone expect you to successfully get a 16-month-old to cooperate for the tube -- it's hard enough to get a small person to sit still for the entire duration of a nebulizer treatment the right way!
I SO don't get the tube vs. mask thing that I'm wondering if you misunderstood the directions. I would def. be talking to the doctor -- even if it's to say, "I'm using the mask because she's getting nothing using the tube. I want her to get at least some of the medicine in her lungs!"
BTW, just some ideas about the nebulizer in general: it's not fun to sit for the 20 or so minutes it takes to get an ampule of albuteral inhaled. The thing makes noise and it has to go on the face -- lots of reasons for kids to resist. She's old enough, I would just say, "This is a way to get medicine in your chest so you can breathe better" and put on a movie and sit her in my lap and not let her wriggle free. After a while, they give up trying to get away and just accept it. But that's with the mask... Also, don't be surprised, once you DO finally start getting the medicine delivered into her lungs (and therefore her bloodstream) if she's not a little cranky/agitated/"off" from the albuterol -- even changing from the inhaler to the nebulizer. And if he's put her on prednisone on top of it, you're in for a double-whammy. Whey don't you go to your pharmacy and talk to them about side effects etc?