The people alleged to be Timothy Mather's wife include Catherine Atherton and her sisters Elizabeth (who is probably her twin although some say they are the same person.) and Isabele. Elizabeth Weeks born 1653 who is the daughter of Elizabeth Atherton's and William Weeks (also spelled Weekes) is also alleged to be Timothy's wife. William Weeks niece, Elizabeth weeks born 1657 daughter of William's Brother Ammiel is also alleged to be Timothy's wife.
Another Elizabeth Weeks born in 1630 daughter of another Ammiel Weeks is also alleged to be Timothy Mather's wife but I think the dates are wrong and they are referring to Williams niece. The old Dorchester burial ground had a Elizabeth wife of Timothy Mather dying in 1709 (or 1710) at the 79 years of age. Being born in 1630 would make Elizabeth daughter of Ammiel the right age but I can't find any other support for the Idea that an Elizabeth born 1630 daughter of Amiel Weeks really existed. Most people have Elizabeth and Catherine Atherton being born in 1628 which would make them older than 79 in 1710. Isabelle was born in an appropriate year to be 79 but her name is not Elizabeth.
There is a pretty clear indication that another Timothy Mather was born in Dorchester in 1649 but there is no clue who his parents were. Elizabeth 1653 Weeks probably married this Timothy Mather.
Elizabeth Atherton was producing many babies with William Weeks at the same time as Catherine was producing babies with Timothy Mather and Isabelle was producing babies with Nathaniel Wales.
My feeling is that if any Isabele Atherton married a Timothy Mather that it was a different Isabelle Atherton and a different Timothy Mather and the genealogy saying otherwise is bad genealogy.
Elizabeth Atherton would have been Elizabeth Weeks after her husband and sister died. She probably married her brother in law Timothy Mather at that time. Most of the alleged marriages to Timothy Mather take place on March 20 of various years. But then who died in 1709 and who did Ammiel Weeks daughter marry?