What was the motivation for many churches to alter the traditional basic basilica plan by adding transepts with eastern chapels that led to an ambulatory with radiating chapels around the apse?

The churches need to accommodate pilgrims. Thirty-five of the Pilgrims were individuals from the radical English Separatist Church, who made a trip to America to get away from the ward of the Church of England, which they discovered degenerate. Ten years prior, English abuse had driven a gathering of Separatists to escape to Holland looking for religious flexibility.