There's so much to this that one can't cover in a single comment, but I'll adress your points. For what it's worth, I agree with the parent that whether Avery is guilty or not is secondary to the miscarriage of justice that has clearly happened.
The physical evidence on the car itself is suspicious: (1) there were no fingerprints, yet there were blood; (2) at least one smudge looks _exactly_ like a bloodstain would look if you applied with a Q-tip [1]; (3) from the armchair perspective of someone who has only seen the not-terribly-high-resolution photos, Halbach's blood looks rusty, whereas Avery's blood looks bright red, almost a week after supposedly dropped there (EDTA-preserved blood does not fade like normal blood); (4) the dashboard blood is unlikely given the position of the cut on Avery's hand [2].
What Kratz claimed was "sweat DNA" (there's really no such thing) on the hood latch was only speculated as such, and was never entered as evidence in the trial because it was considered contaminated; the technician did not switch gloves after examining the inside of the car and then touching the hood. It's worth adding that it's evident from transcripts that the investigators certainly imprinted Brendan Dassey with the idea that Avery had opened the hood; this is also the case with the other details that Dassey comes up with that match the investigator's evidence. Don't forget that Dassey also said a ton of things which could not possibly be true, such as Avery cutting Halbach's throat in the bedroom. (The investigators also tried to get Dassey to confess that Avery had molested him; they quickly give up when Dassey describes Avery playfully trying to grab his genitals during play wrestling. Yet the molestation part has been repeated by the press.)
The key found in Avery's trailer is also highly suspicious. (1) It was supposedly found after numerous searches, and the investigators claimed to find it only after violently rattling the bookcase they claimed it must have fallen out of, despite the photo evidence showing that it could not possibly have happened that way (notice the coins on top of the bookcase). (2) The key was a spare; at least one photo shows that Halbach had a larger keychain, never recovered. (3) Only Avery's DNA was recovered from the keychain, but no other DNA, not even Halbach's.
As for the calls, prosecution tried to frame the narrative to make it seem Halbach was extremely uncomfortable with Avery. However, she had visited his home many times, which easily also explains why he specifically requested her. She would have known that the seller of the car, "B. Janda", was Barbara Janda, Steve Avery's sister and immediate neighbor. The only evidence of Halbach's "discomfort" was that she had once told a colleague about how Avery had once opened the door wearing only a towel, which she found distasteful. Apparently Avery frequently hid his caller ID; he also called her with caller ID. This isn't even circumstantial.
There are a bunch of other points, not touched upon in the documentary, worth adding: For example, the prosecution clearly were not able to determine where the crime scene was — the lack of blood evidence shows the garage could not possibly have been the place of the murder. There are several clear signs that she was murdered elsewhere, and also that she was not burned next to Avery's house. The sheriff ignored an anonymous letter, received early in the investigation, stating that the smelter had been used to burn a body the night following Halbach's disappearance. The woman who found Halbach's car specifically requested (and was the only one to do so) to be permitted to search the Avery property, and she found the car after just a few minutes of walking among hundreds (or thousands) of cars, which seems too absurd to be a coincidence. And so on.
A lot of good discussion is happening on Reddit [3] these days, most of it pleasingly level-headed.
[1] https://i.imgur.com/4VXXzvB.jpg
[2] https://i.imgur.com/Br9KET3.png
[3] https://www.reddit.com/r/MakingaMurderer/