Battery powered project with multiple voltages
In the end, the most simple solution is usually the best. Let's try to sort your needs out.

1) You need a beefy power supply for a motor, 12V-ish. Fine, you have this sorted out already.

2) You need to power the Hall sensor. Why not power it directly from 12V, if it's 5-25V rated? There can be 2 minor difficulties there :


Connecting Hall sensor output to mcu input. If the output is open collector, that's obviously fine as-is. Otherwise, depending on the operation frequency and the mcu input's impedance requirements, the 12v logic out -> 3.3V mcu in connection could be as simple as a large enough resistor, input is then clamped by mcu input diodes. 
Current draw from hall sensor at 12V. That's up to you to determine if it is acceptable. If you need to power it off when dot doing measurements, that's a bit more involved but can be done easily.


3) MCU power can be done simply with a 3.3V buck regulator. Google "low quiescent current buck regulator" returns LT3991 as the second hit, Iq=2.1µA for 12V->3.3V. Then it's just a matter of putting the mcu and peripherials to sleep most of the time, which you'll need to do anyway.

In the end, I think there is NO WAY a second battery with holder can be more efficient for a given battery life, be it weight-wise, volume-wise, and even price-wise, than a simple switching regulator and slightly larger main battery. The only exception I can possibly see is if you need galvanic isolation and low RFI - totally off topic here.