Two ROMs are provided, which differ only by the MBC configuration selected in the header. mbc3.gb specifies MBC3+TIMER+BATT, while mbc3-withram.gb additionally requests 2 KB of battery-backed RAM (which aren't used).
This is because, during development, I have encountered emulator bugs where the behavior of the RTC was dependent on whether RAM was present. They have been fixed now, but your testing target might have its own share of oddity in this area.