First of all, what you describe is not very clear. There is uncertainty in what the problem really is and what level of electronics knowledge you possess. That is overhelming the brain with complexity of variations and possible answers. I suggest you draw a schematic and give some more details.
Anyway, I will explain what I think about such problem in general. You want to read some other device's signal with your MCU on a isolated, battery powered device. First step is to ask questions:
1. What is the signal? Shape of waveform, amplitude, frequency, impedance, external noise, how important is keeping the jitter low, things like that.
2. What is the input? For example, if it is MCU powered from 5V it's digital inputs will expect 0-5V logic levels, also, what is distance from source, etc.
3. Based on 1 and 2, do you need any signal conditioning / conversion? For example, level shifting, schmitt trigger, etc.
Based on answers to these questions define the requirements and a plan to meet them.
The only options after that are to make signaling electricaly isolated or not. Isolated way would be for example using optocoupler. Non isolated way would be to just wire it directly (or through some signal conditioning / conversion circuit if needed). Often there is little point to create isolated signaling to a device which is already isolated. Furthermore, to drive optic transmittion, you would most likely need to take power from vehicle (which contradicts your requirement of not taking it) or otherwise it may load signal source too much (if you would try to drive optocoupler's LED directly from signal source).
About differential ideas. If you wire a signal to an isolated device which does not share nothing else with the source device, then it IS differential. Should not be confused with differential signaling, which could be used, but seems to be not related to the main problem. There could be unequal capacitive loading on a positive and negative signal wire, but lets ignore this for a while.
Why it is differential? Imagine you measure voltage with a handheld battery powered multimeter. Can you connect it's positive and negative leads to anywhere you want on a circuit? Well, yes you can. What it will measure? Potential difference between two points. It will not care about absolute potential in reference to ground. Your multimeter beeing isolated will happily "ride" any DC or AC absolute potential, while showing difference between two points. Also it does not matter what batteries and what voltages multimeter is using itself.
Next example - scope. As you know, scope has it's ground lead referenced to mains earth. So you can not connect this ground lead to any point you like if the circuit you are probing is also referenced to mains earth. You will create a short. But imagine that you need to connect your scope ground lead to something which is at +10V potential. You use differential probe, which gives isolation. None of it's leads is referenced to mains earth, it just measures the difference between two probing points.
Your battery device is same as a handheld multimeter or a differential probe. If it is isolated, you can connect it's internal "ground" to something which is at +10V absolute potential, nothing will happen. You can even connect it's "ground" to signal, and it's "input" to ground (you will measure inverted signal that way). In fact, you can do almost whatever you want. In all cases you will measure difference.
Now the tricky part. Some circuits may be sensitive to capacitive loading. And your device (like any device) will have some capacitance to ground. It will also be picking up external noise quite well and introducing it into the circuit like antenna. For sensitive circuits you may need buffering or isolation to minimise this effect.
For safety, you may want series resistor at the signal source (if it will not damage signal integrity). This may prevent damage from accidental signal shorting.