It can awaken by either a button press, or a number scheduled events which is what the RTC is there for, and my intention is to use the watchdog timer with an 8 sec interval such that it wakes, and based on some multiple of a counter will check if a event should occur every 5 minutes or so, otherwise it will go back to sleep.
In this case use a DS3231, it has two programmable alarm times with an appropriate signal output to wake your microcontroller at time. This way you can save a lot of wake-ups and a lot of battery power.
I see the note on turning off the I2C pull-ups though there's no mechanism suggested. Could this be as simple as attaching the pull-ups to the digital pin (in his schematic below, D8) used to power the RTC without using the 220R resistor to reduce the voltage?