Steve (Audioengr), I'm not sure that we're interpreting the question the same way. My interpretation is that what is being asked is if playing a computer file from a computer-based source will sound any different depending on whether the physical CD that was ripped to create that file had previously been treated in one or more of the ways listed in the OP, or had not been treated. Assuming bit perfect ripping, of course.
Although I certainly agree with everything you have said in your two posts above, effects that occur when CDs are being listened to don't relate to the question as I interpreted it.
Regards,
-- Al