I use a slightly different circuit with the MCP79410 to control the EN line on the Boron. It also requires a NL17SZ74 flip-flip, some N-channel MOSFETs (2N7002) and pull resistors.
Using this circuit the idle current drops to around 75 uA which gets pretty good battery life. This is only recommended for long sleep durations; I wake once a day.
It does not use an external coin cell or supercap. The VBAT pin on the RTC and VCC on the flip-flop connect directly to the Li+ pin (no regulator required).