Seems that SAM51 Micromod has a bug in FLASH connection. See topic “SAM51 MICROMOD FLASH” in SparkFun Forums. If there will be a new version of SAM51 MICROMOD, then perhaps VBAT connection could be modified. SAM51 has a VBAT pin (PB03). This pin would be a natural option for RTC_3V.
BUT, please notice that SAM51 version A has an Errata item “VBAT Mode”. So please assemble SAM51 version D instead of version A. See Microchip document “SAM D5x/E5x Family Silicon Errata and Data Sheet Clarification” for more information about Errata item “VBAT Mode”.