I should start out by saying I don't run pixhawk, but your post has gone a whole 30 minutes without being replied to which is unacceptable!
So if you are going to add a gps and do anything autonomous, then you also need to install a radio modem and have a live connection to qgroundcontrol (or mission planner depending on which firmware you run.) With your ground control software you can see a live report of the number of satellites your gps is tracking. If it's a fairly current ublox8, I'd like to see 7-8 satellites before I'm comfortable flying. Often in flight (with the ublox8) I'll see 12-18 satellites and then I feel really comfortable the system is locked in.)
One issue with any of these systems is self-jamming. You might have an FPV transmitter and your data link transmitter on your quad. Even though these aren't necessarily transmitting on gps frequencies, having a transmitter antenna close to your gps antenna can wipe out the gps with too much noise. Good separation between your gps antenna and all your transmitting antennas is important. My personal rule of thumb is at least 6" between gps antenna and a 100mw transmitting antenna (more if I'm transmitting at higher power than 100mw.) It can be challenging to create this much space on a small quad, so you have to start making compromises, and that's where problems can happen.
So those are the two big issues I'm aware of with flyaways: (1) taking off before you get a good gps fix, and (2) some degree of partial self jamming your own gps receiver.
Historically flyaways have also happened due to firmware bugs or poor handling of gps errors, but I would think most of those issues would have been worked through in most popular firmwares by now.
I do mostly fixed wing UAV work at the U of MN UAV lab so I know a couple things, but only within my narrow little slice of life. We have our own in-house developed flight controller and firmware/software stack which we like, but it is mostly focused on fixed wing aircraft right now. Hopefully a pixhawk/quad expert can jump in and offer more specific advice!