Let me see if I can help a bit
1. There are 2 DAC chips inside the m3x, one for each channel and each with its own Amp (opamp). But on a single ended output (Unbalanced / SE / 3.5mm), the 2 channels share a common ground and the signal will pass through only one amplification circuit. The default setting for the 3.5mm jack (Unbalanced / Single Ended) is single DAC mode. With the M3X and other recent players you can choose via software toggle to enable both DACs, but you'll still only get the benefit of a single Amp. Through the 4.4 jack (Balanced) both DACS And both Amps are always used with one DAC and one Amp for each of the lefft and right channels. If you look at the spec sheet, you'll see 3 levels of output power and 3 levels of battery life. SE 1 DAC / SE 2 DAC / BAL. That's because with each of these settings you'll be using different levels of output power and thus battery. Actually there are 6 levels of power and battery because for each of those modes, you can also select between high gain and low gain. All of the power output specs are showing Max Output Potential which means it's based on high gain. All of the battery life specs would be based on low gain (low gain = less power output = less battery consumption). I don't know what kind of earphones and cable you are using but I'll assume you have a single ended 3.5 cable. If that's the case you are not getting the full benefit of the dual dacs, amplification circuits and channel separation. On M5s, I used the balanced output 90% of the time, but if I want to extend battery life, I'll plug into the the 3.5 jack and it's still a perfectly satisfying experience BUT balanced is fuller, and more detailed. I also the 3.5 out to plug into external speakers, my car aux in, etc..... You will definitely hear a difference between single DAC and dual DAC, because your channel separation will increase along with a moderate amount of output power - though you are still restricted to the single Amp. If you want to hear and even bigger difference in sound, swap cables to a 4.4 (or a 2.5 with a 4.4 adapter) and you'll get both DACs and amps and double the amount of power along with much better channel separation and presumably wider stage.
2. A low pass filter allows all frequencies below a certain set threshold to "pass through" while blocking frequencies above that threshold. So a low pass filter will attenuate some of the high frequencies depending on what the threshold is. If you hear sibilance, enable it.
3. Vehicle mode, when enabled, tells the unit to look for power from the USB port and automatically turn on the unit when detected. I have this on both my BTR3 and UP4 which I have permanently installed in my vehicles. I turn on the car, aux power flows and the unit turns on. I turn off the car, aux power stops and the unit turns off. I start my car, the BTR3 automatically powers on because accessory power starts flowing to in and my phone then autoconnects to it and I'm ready to stream to my car audio without having to fiddle with buttons or switches..... That's Car / Vehicle mode.
Hope this helps.