Yes, there can be more than one lead to an expanded affiliated group (EAG). Each lead will submit a separate registration and add its own members to the FATCA account. On question 13 of the registration, each lead identifies if it is the common parent entity of the EAG.
Sources:
§ 1.199A-12. Expanded affiliated groups.
News Analysis: Who's in a FATCA Expanded Affiliated Group?
§ 1.7874-12. Definitions.
§ 1.1502-1. Definitions.
§ 1504. Definitions