How can I regulate ultralow voltages?
You could try a schottky diode in shunt with the converter input. That would hard limit the voltage to about 400mV, and take negligible current below 250/300mV. I notice from the data sheet that the abs max input voltge is 2v; maybe  you could use a big silicon diode, or a power transistor connected as a diode (base-collector connected together) to limit to 0.6/0.7v without blowing it up?

As an alternative, a series regulator element to consider is a depletion mode FET, one that is on for zero bias and requires a bias to turn it off. Being a FET, it's resistive, so no PN threshold to overcome. When you have minimal voltage from your power source, it will be on. You only need to turn it off once you have the bias available to turn it off. This relies on the rise of voltage at the input being slow enough that the output can bias up, and provide the power to regulate the FET. As it's a series regulator, it won't burn more power than it has to.

An alternative shunt element with better regulation than the diode would be an enhancement mode FET, much more easily obtainable than the depletion type. This is off when unbiased, allowing the input voltage to rise. Again once the converter is producing output, this can be used to drive an op-amp to sense the input voltage, and bias up the FET to shunt at 499mV. You can get 'logic level' FETs, specified to be fully turned on by less than 5v on the gate.