I think you're equivocating between two meanings of the word "converted".
Assuming the laser mechanism is working correctly, the 1s and 0s the DAC is receiving from a CD, or from a wav rip of the CD being transmitted over USB, are identical. There is no format conversion going on.
The physical signal is being transmitted over different connections but this is not what "conversion" means when we're talking about audio information. There's no 'conversion' of the 1s and 0s into a different format before they're reaching the DAC.
There's nothing 'magic' about digital audio. Your input is 1s and 0s, and your output is an analog waveform. If your 1s and 0s in are the same, and your analog waveform out is the same, then what you have is the same, and any perceived difference is entirely in your head. If you feed a DAC 1s and 0s over USB, directly off a CD, over an optical SPDIF connection, or via any other source, if the 1s and 0s hitting the DAC are the same, the output's going to be the same.
In this case, unless you can provide some evidence that the Marantz player is doing some kind of processing and format conversion on the USB input it's not doing on the CD input, then the output, from a 16/44 signal, will be exactly the same.