Learn English – On the top of the hill/ at the top of….. Here, are AT/ON interchangeable

Short answer: The word "in" is idiomatic with corner, so I see nothing wrong with the author's wording.

Longer answer:

I was taught that you should say at the top-right corner of something

I don't know where you learned that, but always be skeptical of a simple rule that always tells you which preposition is right – particularly if you think any other preposition would be wrong. These little words are more flexible than a gymnast!

Even without the word corner, I think I prefer in over at or to, although none of these seem "incorrect":

The logo is a tiny picture that sits in the top left.
The logo is a tiny picture that sits at the top left.
The logo is a tiny picture that sits to the top left.

The only 100% accurate, hard-and-fast rule is that there is no 100% accurate, hard-and-fast rule. I can use several prepositions to accurately describe the locations in this picture:

1. The logo goes at the top left
2. The site name goes at the top beneath the logo
3. The site branding goes in the center at the top
4. The site utilities go in the top-right corner
5. The navigation bar goes below the header and above the body
6. The section navigation goes in the body to the left

However, these are okay, too:

1. The logo goes on top and to the left
2. The site name goes in the header below the logo
3. The site branding goes in the middle above the navigation bar
4. The site utilities go at the top and to the right
5. The navigation bar goes between the header and the body
6. The section navigation goes at the left of the body

"The bird is over the building,"

I would rather say "The bird is above the building" instead of that.

Meanwhile:

On top of talks about position,

Over is direction.