Power flows from up to down, and signal flows from left to right. You mostly follow this convention, but you could improve things in a few spots.
I generally also prefer to use global labels in KiCad, since they allow me to indicate in which direction the signal is flowing (see attachment). This is just personal preference though.
What is the "-BATT" and why have it if it is equivalent to GND?
At first glance, 33u seems huge for the LM2731 boost, especially with 1.6MHz switching. Did you follow the "Detailed Design Procedure" in the LM2731 datasheet? Is it the right value? You display claims to have a typical power consumption of 18mA.
> It might be more efficient to drive directly from VBAT
Nope. The SYS pin on the bq25895 says it's connected directly to the battery unless Vbat is under 3.5V, in which case Vbat is boosted up to 3.5V.
For a design like mine that is primarily going to be low current + low voltage how important is the inductor & capacitor sizing?
Too big and it's going to increase the board size and cost. Too small and it won't work.