From Fundamentals of English Grammar (Betty Azar - pg.163- exercise 10)
3) Newspapers report events that happen ___________ the present. (answer: in)
4) Last year, I was a junior in high school. __________ present, I am a senior in high school. (answer : at)
5) I am a student __________ the present time, but I will graduate next month. (answer: at)
I think the difference is that at present specifies a point in time.
At present I am typing this. In five minutes I will post it.
In the present is less specific. It simply refers to the immediate moment, whenever it may be. To tell the truth, I would not be likely to use it in a sentence like your sentence #3. I would be more likely to say "Newspapers report events that are happening currently", or something like that.
Here one example of how I would use in the present.
My dog always lives in the present.
That means, he doesn't worry about the past or the future. He only responds to what is happening now.