If the book had been compiled even earlier, for example by Mary Brookfield (see image upper/center), chances for misnaming the sitter might have been reduced. However Mary was young when her mother Phebe passsed away and I believe it was at this time point that information on the portrait became vague; but the most important fact was preserved, the name “Samuel Meeker.”
Emma (mom's "gt auntie"), bless her, tried to compile the tree back to Samuel as best she could, but determined that Samuel Meeker was the father of Phebe. [As I know now, Samuel and Phebe were twins.] Emma thus placed the time of the portrait a generation back in time. Which is why she/other family members most likely thought it was by Peale (a famous portrait painter in Philadelphia but a bit earlier than Stuart.) Possibly Emma had come across the more renowned MAJOR Samuel Meeker in the history books of the region, and plausibly thought that such an ILLUSTRIOUS war hero would be interested in having his portrait done to preserve his likeness for posterity.