It looks like any kind of power management on the Beaglebone Black board might be a waist of time.
I see the LDO4 (VDD_3V3A supply) is connected to the enable pin of the external 3V3 regulator U4. Probably with the intention of shutting down the 3.3V supplies when LDO4 is shut off.
Indeed you can shut off LDO4 but unfortunately when the LDO4 pmic regulator is disabled, via software control, the VDD_3V3A supply still hovers around ~1.2v. This is too high for the U4 regulators enable pin and the regulator stay enabled (on).
Even though I understood there is a bleeder resistor in the pmic when the LDO is disabled I guess there are some sneak paths to the CORE (1.1v) supply with all the other stuff hung off the VDD_3V3A supply.