I'd have to look into the components a bit more, but my theory is that the older computers with 4.5V battery backups had a 5V CMOS chip acting as the "power manager"(ie soft power, Real Time Clock, ADB in some of our macs). 4.5V represents the low end of a 5V +/- 10% rail. Most of the pre-mac 8-bit machines(Like the Apple II) used exclusively 5V Digital logic(as well as +/-12V analog circuitry).
Later machines, including many Macs, had mixed 5V and 3.3V logic as 3.3V was sort of new in the late 1980s-early 1990s. The lowering of voltages(particularly core voltages) was all part of the quest for faster speeds and lower power(power is related for frequency and voltage squared - so if you cut the voltage in half, the power is quartered!). Many of our later Macs(Like the Classic and the LC) likely have 3.3V CMOS power management circuits. The cells are 3.6V to allow power "OR-ing" through a schottky diode network, which typically have a 0.3V drop associated. This allows a circuit which will not draw the battery down when the unit is plugged into the wall. Having said that, I'm not sure why some later LCs and even PowerMacs had the cube shaped 4.5V battery. Perhaps those also had a step-down regulator which allowed the battery to last longer due to a much higher margin(the 4.5V battery would have to drain until it's voltage was below 3.0V before you lose functionality). I do recall seeing some power conditioning circuits on the battery in some of the older Mac schematics I've looked at...
Anyway, i'd be careful using any lithium battery where the alkaline was as there may not be the proper circuit protection to prevent current from flowing the wrong way and a lithium battery contains more "violent" chemistry(thats why you get more energy storage in a smaller package). It's possible that the alkaline based system allows some reverse trickle current to lengthen the life of the battery(alkaline batteries can be sort of recharged or at least maintained by very small current injection). I'd have to look over the 512K Mac Schematic I have to see what the battery/main power merging looks like to be sure...