In short, the VB will still run until around 5V, but that’s bad for the batteries. If you cut it off sooner than that, then you have to decide if the low-battery indicator is worth keeping. It’s a very interesting discussion, and it’s something that’s definitely doable with some tinkering.
If the VB still runs under 5V you can use lifepo4 cells as long as the VB dosent run under 4V because the Cut Off from Lifepo4 Cells are 2.01V as absolutely minimum. Best would be 2.5V (per cell) but for the cells its also ok to drain them to arround 2.2V without much lifetime loss. But under 2V the cells will damage itself rappidly. So if the Cut Off from the VB is arround 4-5V you can use 2x Lifepo4 Cells and you are safe without any other Hardware that manage it and you can also use the low battery signal from the VB.
But if the Low Battery show off you did not have much time before its off because everithing under 3V runs verry fast to under 2.5V.
The nominal Voltage is 3.2V and you can charge them up to 3.6V but after charging the Voltage rund fast back to ~3.2V and there it hold it over ~85% of its capaticity and then it will run fast its last 5-10% to under 2.5V.
I would prefer lifepo4 because they have much more lifetime then liion or lipo and they are also much safer because the cant explode.
You could bypass the onboard 5v regulator and build your own high efficiency boost-buck switching regulator, combined with a rc network for the delay power good signal. Combine this with a lipo charging circuit and a usb c port and that takes care of powering and charging the system.
Could most likely smash together something of the shelf to do it to.
And a handheld is a great place to try that, since otherwise you’d have to modify the controller AND the head unit, creating a head unit and controller that only work with each other and no other hardware. In a handheld, they’re permanently married anyway.