It is with respect to ground, the positive pole of the battery is connected to ground.
The telegraph system figured this out very quickly. Most water in nature has at least a bit of salt in it, which is present as positive sodium ions and negative chloride ions. By making the outdoor wiring negative with respect to ground, the chloride ions are repelled, and such wires corrode much more slowly than those that're positive with respect to ground.
Since most of the telegraph network, later the telephone network, is outdoors, this is a pretty big deal.
You tie one of the leads to earth (literally grounding it)[1], leaving the other non-grounded. Depending on if you tie the negative or the positive lead to ground, you get 48V or -48V with respect to ground. As long as the potential between the most positive lead and the least positive lead is 48V, the circuit itself doesn't care.
As mentioned here[2], the reason for grounding the positive lead is to prevent galvanic corrosion[3] destroying the buried copper.
Generally with respect to ground. There are many good reasons to connect your power system to ground and so this is commonly done. (there are pros and cons to connecting to ground, but it gets complex fast)
No. In telco, the -48V is referenced against ground, like the physical ground. If you're isolated, you can do this. but they would still need to be referencing the 'ground' to something ... likely the negative side of the main battery pack.
The reason why -48V is used is because it is provided as a bias voltage to give wiring cathodic protection, to prevent corrosion of telecom infrastructure. If you used 48V, it would not work. You need a negative voltage referenced against ground.