Track start and stop timings for SACD rips performed by PS3 and SACD_extract (or similar software), are determined by the PQ markers embedded in the cutting master for SACD production. Those markers are intended to run the SACD player display metadata, and have no actual conection to the music content, other than where the mastering engineer placed them. Normally that's about one second prior to music start. It's simply a situation of where the extract software used to facilitate automatic track slicing of the continuous album file uses data (PQ markers) not intended for that purpose.
Sonoma track starts and stops are determined manually by when the Record button is hit. The SACD transport is free running, and has no control of Sonoma's operation. So therefore some time buffer amount is usually built-in. Like I start the Sonoma's Record, then hit Play on the transport.
So in Bruce's examples, some PQ Marker(s) are within the music content, and therefore the track data prior was not included in the track by the SACD_extract software. Also, PQ markers are both Start and Stop types. Most DSD edited masters I work with have an album beginning Start marker, then more Start markers at the beginning of each new track, and a Stop marker at the end of the last track. But sometimes the mastering guy put a Stop marker at a track end, followed by an inter track time, then a Start marker at the new track beginning. I have no idea how SACD_extract treats these occasional Stop markers, and whether it cuts out the time between the Stop and succeeding Start marker when slicing.