About the Li-ion battery, it seems to be a general agreement (see this topic for example) about the fact that the best option to power a node is with AA or AAA batteries. In fact one of the advantages is that you don't need to step up or down the voltage to power the radio and the MCU.
There is no one "best option". The power supply heavily depends on the project requirements. The PIR sensor requires noiseless voltage between 2.7 and 3.3v. This makes use of 2xAA problematic. In my opinion for such a project higher voltage supply with low quiescent current ldo is the best option. And it happens that li-ion battery with its voltage range and 3v ldo makes them perfect match. At least this is how I did it in my homE I went even further in my project and there is two ldos, one for pir and one for mcu + rf module as those two components creates large spikes in current flow as they work making supply voltage noisy.
PS. The other benefit of rechargable batteries is that they are rechargable so you don't need to remember to buy batteries when you go out of them.
you will handle the pir in your software but generally the pir needs to be powered all the time so no need for shutdown mode in your boost converter. The other thing is that pir doesn't linke noisy power supply, and dc converters are rather noisy especially in low current area. I would recommend t