In what manner does the Cockpit Voice Recorder timestamps?
As described, it is the flight data recorder time. The linked video in that Wikipedia article shows it as seconds. I could not find after how much time Flight 593 crashed, but 2400 seconds equal to 40 minutes.

An FDR typically records around 90 parameters, and certainly can and does monitor all of them all the time, even when several parameters change within a single second.

For the purpose of transcript for this accident, the article on Wikipedia (which is far less technical and detailed than an NTSB investigation report) omits all the entries from FDR recordings which are neither relevant to the story, nor interested to the reader. For example, the reader will care less the input from different sensors between 2303 and 2314.



Since the recording time of a CVR (30 minutes - 2 hours) is less than an FDR (25 hours), they are synchronized for an investigation. This is described here (PDF), for the investigation of Flight 1549:


  The CVR and FDR data were synchronized to one another by comparing the
  FDR “Key VHF” parameter with radio transmissions as heard on the CVR
  recording. By comparing the CVR elapsed time (time since the beginning
  of the CVR recording) for radio transmissions to the corresponding FDR
  Subframe Reference Number (SRN) for “Key VHF”, a relationship between
  the CVR elapsed time and the FDR SRN time can be developed.