Having watched it, do I think their relationship is the most toxic? No, of course not. The title is obviously just clickbaity hyperbole. I do, however, think I get where Alteori is coming from with some of her points.
Firstly she was getting at how Ali initally was with Littlefoot's friends. It's not a good thing to pick out one person of a group to play with and then exclude the rest of the group because you don't like them for whatever reason. But then I can understand where Ali comes from with her fear of other kinds since she lives in a large longneck-only herd and has probably only interacted with other longnecks before. If the first film was any indication, Ali was probably taught the same as Littlefoot about the kinds all keeping separate and may have thought she was doing something wrong if she interacted with the rest of the gang. Littlefoot on the other hand had to team up with the others in order for them all to survive (remember he repeated his mother's words and initially rejected Ducky), as did the adults, so they learned to put their prejudices aside (well, mostly...

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There's also her point that Ali is really clingy with Littlefoot which I do sort of agree with, but then again she seems to be the only child in that longneck herd that we see and so she was probably pretty lonely. She probably would have been really excited to see another longneck her age in the valley she could play with, so naturally she'd want to spend as much time with him as possible.
Then there was the part where Littlefoot went up to her to ask her for directions to the land of mists so he and his friends could go, and then she gets a bit weird about it. She says she doesn't want to go, and then as soon as he mentions taking his other friends she says she'll go but the others can't come. That could be interpreted as Ali being quite possessive of Littlefoot and manipulating him into staying away from his long-time friends. But again, she's a child who's come from a traditional longneck herd who promote being only with other longnecks. She's probably projecting these values onto Littlefoot because she thinks him interacting with other species is wrong. She's ignorant, but of course she is because she hasn't been exposed to different ideals like this. In the end she realises that she needs Littlefoot's friends to help them get all the way and she grows and develops as a character.
I do get some of Alteori's points but I think she doesn't go into understanding why certain characters do certain things. It basically boils down to 'she's toxic because she's clingy and keeps Littlefoot away from his friends because she's racist' but that was the point. Ali was there to cause a rift between Littlefoot and his friends, but she didn't do things that annoyed both the gang and the audience because she's a bad person, she did it because she was ignorant. She wasn't intending to be toxic, she was just projecting the adults' values on Littlefoot, just as Littlefoot himself had done when he first met Ducky. She was scared of a situation she hadn't been put in before and did what she could to avoid it, while making Littlefoot do the same because she wanted to hang out with him as another longneck her age. But then by the end of the film, she's not like that anymore, because she has to team up with Littlefoot's friends and realises that they're not so scary after all. She develops as a character. If she had been exposed to other kinds before going to the Great Valley and knew it was okay to hang out with them, and then manipulated Littlefoot into staying away from them in favour of her, then yes I would agree she's toxic, but that's not the case here.