I suppose it is worth pointing out that although both a cd and a turntable spin a disc and 'read' it, any similarity between how they work ends there.
The better the TT, arm and cartridge, the better the 'read' of the disc and this will transfer into perceived sound quality. This is not true of cd players. No matter how fancy and expensive the mech it will not read the disc any better that the transport on a £20 DVD player from Tesco. A cheap mech might potentially introduce noise to the signal due to vibration, and this may have an effect on sound quality, but it will not affect how accurately the disc is read.
In digital audio it really makes no difference whether the file is being read from an optical disc or a hard drive, this will have no effect on the accuracy of the read. yes the file is not being read in real time in the way a cd is read, this is why cd players have error correction. if there is a read error the error correction will sort it and you will get a perfect read. if the error correction fails you will get a drop out, or a nasty squeak or similar. it will be obvious. What you won't get is a slightly worse rendition of the music. it will either work perfectly or will not work at all.
Consequently there is no inherent benefit in terms of sound quality using file based audio compared to optical disc based audio.
of course there are many other things that will effect sound quality with digital audio. The design of the analogue output stage and the power supplies do seem to have a major effect, but this will apply to both CD players and a computer/DAC set up equally.
It is regrettable that the emphasis on improving digital replay seems to concentrate on things that don't make any difference to what we hear and little or no attention is paid to the things that do matter, mainly because they are not easily marketed to people with no understanding of how digital audio works, but that's commercial reality.
Regarding upsampling - upsampling a recording is not the same as playing back a recording that was originally recorded with mics able to capture frequencies up to 196khz (or whatever). Upsampling will change the perceived sound quality.
Note I say 'change' rather than improve. Whether you like the change is personal and subjective. I don't like it, for me it makes everything sound 'fluffy' and less defined. The important point is this should not be taken as evidence that so-called 'high resolution' recordings sound better because they contain frequencies beyond 22Khz (i.e the limit of human audibility) since it is not the same thing at all.