Usually you get that track line because there is not a good GPS 3D fix when you arm and fly (and logging starts). The GPS unit doesn’t get a good fix until after take off and away from ground clutter.
If you set these you will not be able to arm until there is a valid 3D fix, which could be the desired behaviour:
FENCE_ALT_MAX,120 <- enter safe values here
FENCE_RADIUS,600 <- enter safe values here
This is not exactly your problem though…
In your case the bad track line, reduced number of sats and bad HDOP, mostly happens at the end of the flight - probably at the same time as you are seeing the ESCs reactivate. It’s like the flight controller is trying to move to where it is supposed to be, given that the GPS is saying it’s now a couple of miles away.
I notice the battery voltage goes quite low. Vcc is not great either. Maybe the GPS unit would benefit from a better Vcc, around 5.0 to 5.3 volts instead 4.85.
See Big GPS Round Up for how the supply voltage can affect the GPS units more than most people expect.
You have some funny things going on in logging too, not sure if it’s a bug or because of the GPS going bad after landing and skewing the time.
I really would persist with upgrading the flight controller and firmware, because the logging is so much better and there are so many improvements.