It's a trick question: I believe you need to use both in your training, or else you're selling yourself short. If you only use one, you’re going to end up with strength (and maybe physique) imbalances that will keep you from reaching your potential.
Now, just like I wrote in my article about high-rep work, you need to be careful when you're incorporating variations of the competition movements in your training, or else you might miss out on a lot of the potential benefits. Here are some things to consider:
Performance standards.If you’re leaning forward and putting a ton of lower back into your high-bar squats, then you're effectively doing some bastardized variation that isn't going to carry over much to your low bar. On the other hand, if you turn the low bar squat into a good morning, you’re probably not going to see good results, either.
Timing. Obviously, if you’re close to a meet, you should be focusing on the lifts you're going to do in the meet. Save the variations for the offseason or early in prep.
Enjoyment. Look, you’re not going to stick with something you don’t enjoy. But there’s a good chance that you don’t enjoy something because you suck at it. As always, balance is key: do enough work to address your weaknesses, but if you hate low bar squats, don’t try to make them the cornerstone of your programming, regardless of what anyone else tells you.