Criteria number 1 : Base-emittor junctions of a transistor that are reverse polarised cannot have much more than 6 volts. They start 'leaking' and accumulate time based damage.
Criteria number 2 : fist logic chips were bipolar and had quite a bit a static current consumption resulting in heat. higher voltage means more heat...
criteria number 3 : early chip technology used for digital suffered from scaling problems. they needed quite a bit of distance to 'hold' a standoff voltage. making chips impractical and expensive ( the cost of a chip is defined in square millimeters of surface... )
Throw that in a heap and you end up with something that works between 3 and 5 volts. At 3 volts the transistors did not switch 'fast' enough to get nice clean pulses so they settled at 5 volts. All criteria met
Now, for early MOS technology they ran into another problem. They only had NMOS transistors. There were no P-MOS ( they hadn't figured out the process of implantation yet, they were depositing doped regions through crystal growth in an oven and then etching it. ) So they stacked nmos transistors to make totem-pole systems. problem is that you now need an additional voltage to switch top and bottom. So they could have used ground , 5 volts and 10 volts ( to turn on the top transistor you raise its gate 5 volts above its source which sits at 5 volts. Problem is that this was not compatible with bipolar logic. so they flipped the stuff around. they used -5 volts and used that as the 'ground' level. to create a compatible output all they needed was a mos from the 5 volts to the output pin. turn on the top mos ang you get 5 volts out. turn it off and you get 0 volts out. the internal logic used -5v as a logic 0 and 0 volts as a logic 1. Early cpu's in NMOS technology actually have a -5 volts pin.
Once they could construct both PMOS and NMOS (what we now call the CMOS process : complementary metal oxide semiconductor : meaning both n and p , although that metal - oxide ... for a long time was not true... it started like that, went away ( we used doped polysilicon as the gate no need for metal.... ) and now is back ) the negative voltage wa sno longer needed.
there were other technologies around like ECL that also required a negative voltage and used 5 volts and -3 volts as their supply rails ( although the logic levels for ecl are like 1 volt and - 1.2 volts or something like that . consumption of power in ECL is a constant , you just throw current from one loop to another) so that way they maintained compatibility with existing power supply systems..
it's all historical and based on practicality for early integrated circuit technology.
A cray computer like the cray 1 for example did not have a 'regulator' as we understand it now. they used a rotary convertor. a motor drove a generator that made a 6 phase output voltage at 400 hertz. they rectified that and ended up with very little ripple due to the 6 phases. so they needed minimal capacitors ( the cray 1 sucked hundreds of amperes on its power rails... being a fully ECL machine )
the 'regulator' just controlled the field coil of the generator to adjust the output of the generator. so they did not use a transistor to regulate the hundreds of ampere. just control the strenght of the spinning magnet an u regulate output voltage of the generator.
there's all kind of trickery like that in these early machines.