Photo geotagging software, that merge external waypoints with photos do it via the photos time stamp. Some match to the closest waypoint, a few will let you interpolate a path between the way points. However this does rely on accurate time stamping on both devices. There are a few things that can conspired to get your devices out of sync.
- Changing time zones, usually smartphones will automatically adjust as you travel into a new time some and the phone connects to a different network/carrier or even the same network in the new location. This is great but your camera won't!
- Daylight Saving, this is a bit like changing time zone, where you smartphone, and computer, probably will but your camera may or may not. Further if you camera does change it might change on a different weekend to the gazetted times at the place you are staying .
- Normal drift in the accuracy of embedded clocks, usually this is only measured in seconds but I just checked and my two computers are 56 second different, my phone a few seconds different again, my canon camera is 5minutes fast and my Pentax 2 minutes slow!! Ok last time I did check their synchronization was last October, in a different time zone.!
It really doesn't matter which is the "correct" time as long as they are all synchronized. A few second is probably not going to make any difference to reliable geotagging if you are on foot. However if you are cycling or drive between photo shots you might find some photos get misplaced.
Most of the geotagging software now does allow for time shifts between the camera and the gps device, but the method of correction is often very confusing.