It reads out the average of the two batteries. I find that to be just fine as the two should never vary more than a few hundreds of a volt if they both start together.
A new SF primary will start at ~3.3v and when they get to ~2.8v they will no longer power the higher levels. It takes a long time to use a set of primary batteries in the SPY. About 1.5 hours on high at 1000mA and many many days on low at 2mA. If you set your low down even lower to the power level of a tritium, it will last even longer but remember the computer is still using some power and that does not change. Chevrofreaks battery testing was done with the old DB converter board. It is not super accurate for the STFu but still similar.
Rechargeable batteries are all over the map and I can't speak to yours. I have one set that are 3.7v when new but the battery meter has an upper limit of 3.75v, it can't read higher so if you test 4v rechargeables you will not get an accurate reading when they are fully charged but you will after they run for a while.