Audio output quality
Unfortunately, the real-world gets in the way - there's a whole host of things between you and the "bit-perfect" waveform that comes from the MP3 decoder:


As you noted, user controllable filtering (graphic eq for example) - this may be disabled.
"improvements" to the sound made in the digital domain (for example compression to make it sound "louder" and bass boosting) - this may also be disabled
The internal processing is often done at a greater bit depth than the output DAC capability - for example, 32 bit processing but only a 16 bit DAC.  There must then be a process to reduce the bit depth.  This may or may not include dithering of some sort.  The results of this will sound different depending on the implementation.
The digital to analogue converters may be of differing quality, which will impact on (amongst other things) the linearity and noise floor of the analogue output.  
The clock feeding the DAC will also have an impact on the performance - higher jitter will be noisier.
The headphone driver will also have various analogue characteristics - eg. noise floor, frequency colouration etc.