The text says Ratanji saw 'Maharaj, the heap of merit' in the Masjid. Is this a reference to Gajanan Maharaj?

No, this is not a reference to Gajanan Maharaj. While the term 'Maharaj' is used, the context within Chapter 14 makes it unequivocally clear that it refers to Sai Baba. The narrative details Ratanji being advised by Das Ganu to go to Shirdi to meet Baba. Upon arriving, he goes to the Masjid for darshan and prostrates at Sai's feet. The very next sentence, as found in Chapter 14, says, 'Seeing Maharaj, the heap of merit, love surged within him.' Therefore, 'Maharaj' is used here as a title of respect for Sai Baba, the specific saint Ratanji came to see in Shirdi.