Depends on the DAP. For instance, when I connect my Rio Karma through the dock and into my HU through RCA inputs, the volume buttons on the Karma only affect the headphone jack. The signal that's going to the HU is not affected by volume modifications, as it doesn't pass through the op-amp that outputs on the headphone mini-jack. So what I'm saying is that I can connect my headphones to my Karma, and connect the karma to the dock; the Karma will put out a signal on the headphone jack (volume controllable) AND will put out a signal through the dock's RCA outputs (volume uncontrollable). My HU has an input sensitivity setting too so that if I have a device which puts out low voltage, it can amp 'em up correctly (i.e., it has a "gain" control, however it's discrete values; low/med/high).
S/N ratio doesn't anything if you aren't into hi-fi, critical listening, which is obvious in your scenario.
The HU doesn't read any "files". All the HU cares about is a fluctuation of voltage getting sent to it. The signal will get "routed" to the speakers (that is, after the HU is done with it). If you've got DSPs, it may have an ADC onboard but then you know it has to go through a DAC in order to output to speakers or its line out. So there's already 3 modifications to the signal: 1) passing through the ADC, 2) the DSPs doing their thing & the final HU stereo mix, and 3) passing through the DAC.