Atmel SAM E70 (ATSAME70Q21, Cortex-M7) battery backup
The idea behind the Vbat input on chips such as the STM32 is that the RTC and other low-power peripherals will normally be powered from the main Vdd, automatically switching to Vbat when Vdd is absent. On-chip, this can be implemented with something as simple as a diode-OR:







simulate this circuit &ndash; Schematic created using CircuitLab

To save pins (I assume), the SAME70 doesn't provide a separate connection for the RTC, instead having it take power from the main Vdd. However, as they show in the datasheet section you referenced, you can add the power-switching logic externally:







simulate this circuit

The schematic you posted is very complicated, because it's trying to do something slightly different: C103 on that diagram is a supercapacitor (100 mF!), so much of the circuitry is responsible for charging it at a reasonable rate. You're using a coin cell, so none of that is relevant.

There are several practical considerations with the schematic I posted. First, I recommend Schottky diodes, because you lose a lot less voltage that way. Second, I assume that you're generating a 3.3 V rail from the USB Vbus with an LDO linear regulator. If so, you'll want to take the feedback for the regulator from after the diode, so that the regulator can compensate for the diode drop. It would look something like this (ignoring bypass capacitors):







simulate this circuit

Third, this will try to power the entire chip from the coin cell when USB power isn't present. You have to be very careful to enter Backup mode as soon as you notice Vbus missing, or you'll drain the coin cell quickly. You'll want to use a GPIO pin to detect VBus (see schematic 2 in section 58.2.8).