Hi,

See JEE Mains is a National level exam which is conducted by National Testing Agency (NTA) 

Whereas AP EAMCET is a state level test which stands for Andhra Pradesh Engineering, Agriculture & Medical Common Test which this year was Conducted by Jawahar Lal Nehru University, Kakinda

Now if we talk about any private university, they are not bound to accept JEE Mains Marks or AP EAMCET marks its up to them if they want to consider the marks or not. The University you are talking about might only be taking admissions in Engineering based on marks obtained in EAMCET.

Suppose you go to some other country and their you say them that i have got full marks in JEE Mains, they won't consider as why would they matter as they donot take admissions based on the marks obtained in JEE Mains.

Hope you get that :)