It is because her framing is from the perspective of Sam's character. She is supposed to unapproachably attractive to give him a huge deficit of confidence and power.
This was my thought too. I remember the iconic hood-lean, but I also remember Fox's character being the courageous, knowledgeable, capable half of Team Shia; with Sam being the inept, basic underdog who served as the audience proxy. I remembered the theme of women being underappreciated, and lots of jabs at workplace sexism all the way up to the manchild Bush-era President; although I'd totally forgotten every significant detail about the plot, and every character but the two protagonists and Sam's parents. I also erroneously remembered Sam's mother being played by Julie Hagerty.
This isn't to disagree with anything Ellis says in her video. I think the issue is less Michael Bay treating Fox as eye candy, and more an issue with his presentation of the movie's plot in general. That is to say, I don't think Bay undermined the script; he just didn't do it justice.
I think the hood-lean shot is appropriate for the scene: Sam sees a woman he perceives to be an unattainable beauty, and ignores all the smart stuff she's saying because he's thirsty and socially inept. This is the one exception to the general sense of carelessness that pervades the human side of the movie: Bay filmed the script he was given in a very pedestrian way, and excelled at capturing that moment of teen lust; but his main focus was always on the OTT CGI action. Bay clearly doesn't really care about the human characters. On top of that, audiences were watching that movie for Peter Cullen's performance. Fox and LaBoeuf and the rest of the cast are there to ground the robots in a basic human story and get them to the next action sequence, while providing comic relief and fantasy fulfillment in LaBoeuf's case, and a sexual goal for both LaBoeuf and the guys-who-like-girls in the audience in the case of Fox.
So here's the way I see it. The script is good, and the characters are well-rounded. The writing generally presents women as overachieving and underappreciated. Bay shoots what's on the page without undermining it. But he also doesn't give a fuck about the anything but the giant robot action scenes. Neither do the producers. Everything around the Transformers is just kind of there. The writers did their job; Bay did his, but he didn't bring passion to the human elements. He didn't care about the characters, and neither did the audience. On top of this, Bay so exceptionally nails that one shot that is purposely representative of LaBoeuf's lust that it stands head and shoulders above everything else.
So people remember Optimus Prime, Bumblebee, and Megatron, nothing about the story (so they infer the actors and/or writing sucked); and Fox's abs. And since they've been conditioned to associate sex appeal with lack of talent and remember nothing to counter this prejudice, they come away thinking Fox must be
especially talentless. Instead of remembering nothing, they remember
sexy.
Obviously the following movies don't have decent script writers grounding Bay's direction the way TF1 does, so everything becomes progressively stupider and more outlandish. And more memorable because of it: TF1 feels like a by-the-numbers modern Hollywood action flick, like Battleship, Jurassic World, GI Joe, etc. TF2 is full of what-the-fuck with its racist robots. TF3 I forget completely, but TF4 has the rape card, Kelsey Grammer making deals with Deceptions, Mark Whalburg's confused face. I haven't seen the new one, but the trailer makes it look nuts - anything but by-the-numbers action.
I don't disagree with Ellis's analysis of TF1 and the effects of the way Megan Fox is presented, but I do think it was more a matter of apathetic filmmaking than Hollywood sexism deliberately undermining the script. I don't think too much weight was given to the shot of Fox leaning over the hood; I think too
little was given to literally every other not-action-scene in the movie. Really interesting to stop and think about this though. I'm going to watch more of her stuff.