Arduino Zero RTC alarm not running loop
I ended up deleting my copy of RTCZero and installing a new one via the Arduino IDE library manager. This solved the issue.

The difference between my local copy and the upstream one is in the standbyMode() function. I had the following PR merged into my local copy of this function:
https://github.com/arduino-libraries/RTCZero/pull/46/files

After I installed the clean copy I went and replaced the standbyMode() function's content with the following:
https://github.com/arduino-libraries/ArduinoLowPower/blob/892594adbccf45b198fc067ea994048c76523936/src/samd/ArduinoLowPower.cpp#L18