OK so here are the exiftool results per your suggestion, for two of the files in question. I ran this on the originals as copied from the CF card, Photos has not touched these yet.
So what is GPStimeStamp and where does it come from? Why is Photos using it? I see in the second example above the time is 12:26:12 and the GPSDateTime is 16:13:38Z. What does that mean? What is the Z?
exiftool -a -G1 -s -api QuickTimeUTC=1 -time:all -api RequestAll=2 5DM40046.JPG
[ExifTool] Now : 2020:12:31 16:28:37-05:00
[System] FileModifyDate : 2020:12:31 12:24:52-05:00
[System] FileAccessDate : 2020:12:31 13:35:39-05:00
[System] FileInodeChangeDate : 2020:12:31 13:22:21-05:00
[IFD0] ModifyDate : 2020:12:31 12:24:52
[ExifIFD] DateTimeOriginal : 2020:12:31 12:24:52
[ExifIFD] CreateDate : 2020:12:31 12:24:52
[Canon] TimeZone : -04:00
[Canon] TimeZoneCity : New York
[Canon] DaylightSavings : On
[ExifIFD] SubSecTime : 00
[ExifIFD] SubSecTimeOriginal : 00
[ExifIFD] SubSecTimeDigitized : 00
[Composite] SubSecCreateDate : 2020:12:31 12:24:52.00
[Composite] SubSecDateTimeOriginal : 2020:12:31 12:24:52.00
[Composite] SubSecModifyDate : 2020:12:31 12:24:52.00
exiftool -a -G1 -s -n -ee '-gps*' 5DM40046.JPG
[GPS] GPSVersionID : 2 3 0 0
[GPS] GPSSatellites :
[GPS] GPSStatus : V
[GPS] GPSMapDatum : WGS-84
exiftool -a -G1 -s -api QuickTimeUTC=1 -time:all -api RequestAll=2 5DM40048.JPG
[ExifTool] Now : 2020:12:31 16:29:24-05:00
[System] FileModifyDate : 2020:12:31 12:26:12-05:00
[System] FileAccessDate : 2020:12:31 13:35:39-05:00
[System] FileInodeChangeDate : 2020:12:31 13:22:22-05:00
[IFD0] ModifyDate : 2020:12:31 12:26:12
[ExifIFD] DateTimeOriginal : 2020:12:31 12:26:12
[ExifIFD] CreateDate : 2020:12:31 12:26:12
[Canon] TimeZone : -04:00
[Canon] TimeZoneCity : New York
[Canon] DaylightSavings : On
[ExifIFD] SubSecTime : 95
[ExifIFD] SubSecTimeOriginal : 95
[ExifIFD] SubSecTimeDigitized : 95
[GPS] GPSTimeStamp : 16:13:38
[GPS] GPSDateStamp : 2020:12:31
[Composite] GPSDateTime : 2020:12:31 16:13:38Z
[Composite] SubSecCreateDate : 2020:12:31 12:26:12.95
[Composite] SubSecDateTimeOriginal : 2020:12:31 12:26:12.95
[Composite] SubSecModifyDate : 2020:12:31 12:26:12.95
exiftool -a -G1 -s -n -ee '-gps*' 5DM40048.JPG
[GPS] GPSVersionID : 2 3 0 0
[GPS] GPSLatitudeRef : N
[GPS] GPSLatitude : 40.31106
[GPS] GPSLongitudeRef : W
[GPS] GPSLongitude : 75.3169183333333
[GPS] GPSAltitudeRef : 0
[GPS] GPSAltitude : 189.2
[GPS] GPSTimeStamp : 16:13:38
[GPS] GPSSatellites : 5
[GPS] GPSStatus : A
[GPS] GPSMeasureMode : 3
[GPS] GPSDOP : 4.7
[GPS] GPSMapDatum : WGS-84
[GPS] GPSDateStamp : 2020:12:31
[Composite] GPSAltitude : 189.2
[Composite] GPSDateTime : 2020:12:31 16:13:38Z
[Composite] GPSLatitude : 40.31106
[Composite] GPSLongitude : -75.3169183333333
[Composite] GPSPosition : 40.31106 -75.3169183333333