My guess was that Peter's wife #2 and wife #3 were both named "Mary." However, your suggestion also is a possibility -- that the relationship with Mary Ann was on and off and on again, with Mary Ann having a child by another man between her two times with Hiram.
There is a 3rd possibility:That Isabelle counted her step-mother as her mother.Perhaps Isabelle's real mother died when Isabelle was young, and Peter's 3rd wife was the only woman she knew as a mother.
I show Isabelle born January 1841. I show Mary Ann's son Ezra (a non-Hufford) born April 1840. If those dates are correct, it's extremely unlikely that the same woman could have birthed those two children.However, if Isabelle's mother died in childbirth or soon after, Peter may have married a woman who had a young baby herself. The result would have been Isabelle having known no other mother. ... It's not inconceivable that Isabelle was born to a wife #2 and never even realized that wife #3 was not her real mother.
Lots of families have lots of weird and screwed up secrets.