No, she is definitely Tiye's daughter, at least the inscriptions say so.
(well... in the novel I'm writing now she is a daughter of one of Akhenaten's elder sister and Tiye pretends that Beketaten is her child 'cause she doesn't want people know that she is an illegitimate child... but it's only my guess
Hi Meritaton, Tiye wouldn't have had to pretend that Baketaten was her child. She could have adopted her. The ancient Egyptians did believe and practice adoption as a means of getting children. Adopted children had all the rights of natural children in Egyptian courts of law.
Sometimes i believe it is this aspect of Egyptian culture that gets so many folks confused as to who is related to who. Sitamun for example is considered by some to be the daughter of Amenophis III and Tiye. While other's believe that she is actually a daughter of Thutmosis IV and youngest sister of Amenophis III. If after her father died, she could have been adopted by her brother and his wife making her sister/daughter of Amenophis, without the social taboo of our time coming into play as great as they normally would.
As for a princess having an illegitimate child umm...
i have played with the position of Divine Wife of Amun as a possible means to disguise the illegitimate birth of a child to an unmarried princess. But then i remember who would tempt Pharaoh in such a manner? I know a very brave man.
The best of success with your novel.