Thanks to Catherine Evans, I re-examined the 1901-1905 Leavitt book. If you go back two pages from the beginning of the Spencer chapter, you'll find the printed tree between two title pages for the chapter, unpaginated, but probably page 351:
Unfortunately, the rest of her chapter on the Spencers does not discuss their English origins at all, but only the New England information.
Jacobus in his 1950 article in The American Genealogist, does not discuss Leavitt's publication. Here's what he does say:
"In 1903, the Rev. John Holding, MA, then Vicar of Stotfold, co. Bedford, England, published The Spencers of Bedfordshire. … tracing it back to one Thomas Spencer who was living at Eton in 1433.
"Some years earlier the noted antiquary, Henry F. Waters, had found mention of the four brothers in the will of their London uncle Richard Spencer, and had published this in the NEHGR and in 1901 included it in his Genealogical Gleanings in England
"In recent years the parish registers of Stotfold and Edworth have been included by FG Emmison in his Bedfordshire Parish Register Series. Careful comparison has been made between these and the entries as printed by the Rev. Mr. Holding, resulting in some corrections and in the addition of two or three important entries.
And elsewhere in his 1950 article, he makes no mention of a) two wives of John Spencer, or b) the possibility of Ann Clark as the spouse of John Spencer. He only conjectures the possibility of Anne Merrill from the language in her will.