All the stuff that's natively 12 volts now could simply have been made natively 48 volts. You can make a 48-volt lightbulb as easily as a 12-volt lightbulb. You can make a 48-volt motor as easily as a 12-volt motor. Actually, motors for higher voltage tend to be smaller and lighter, which is why industry tends to go straight for 4160-VAC motors whenever 480VAC is inadequate.
What applications cannot be made to work at 48? I'm not aware of any. As I said in the comment to which you're replying, the telegraph and later the telephone network had been running similar DC systems since the 1850s or so at various voltages depending on the length of the telegraph line, with the telephone network taking over and 48 volts firmly entrenched by the 1910s. There was a huge manufacturing base producing 48-volt equipment, including motors and generators, indicator lamps, and a mindboggling array of switches, relays, stepping selectors, and their ilk, and all that was before WWI.
Furthermore, Charles Kettering who invented the automotive starter motor (and made it work at 6 volts), was around the same time making Delco-Light plants for rural electrification, which mostly ran at 32 volts DC. These supported a whole line of 32VDC appliances -- lights, vacuum cleaners, kitchen gadgets, irons, motors that could be attached to other machines in the shop. There was also a less common 110VDC version of the system but I can't find any contemporary literature discussing the differences, although I'm sure they would've quickly discovered that the 32V system was pretty docile while the 110V encouraged extreme care around open contacts.
As for why cars didn't use the higher voltages already in use and superior in many ways, my only guess is that a lead-acid battery with a high number of small cells must've been difficult or expensive to manufacture, compared to one with a small number of large cells. The Delco-Light plant used a large rack of 2-volt cells, whereas the starter motor used a single 3-cell packaged battery that fit easily under the hood. If they'd just figured out how to package more smaller cells together....
To convert voltages to useful levels without suffering massive losses in efficiency.
> What applications cannot be made to work at 48?
Basically every logic-level transistor will not work at 48V. It's nice that these last-century analog devices could be made to operate at different voltages: present-day semiconductors are not so conveniently flexible.
Simple physics dictates that required inductors to step between voltages increase in physical size (and weight, and material cost) as that voltage disparity increases. Capacitance required, etc. all increases with it. Efficiency plays into both of these as a triangle. Heat increases as this disparity increases. These properties are unacceptable for a myriad of use cases.
You didn't have to convert voltages all the time for things you did in a car until relatively recently. All the typical 12V stuff could've run at 48V no problem. By the time we wanted to put computers in cars and charge our cell phones, switching supplies were readily available. The only part of the system now that really benefits from lower voltages are semiconductors.
How would they have done this without cheaply-available high-speed switch-mode power supplies with low-DCR inductors/MOSFETs?