These traces were taken a minute or two apart on a 6S+, and despite being all but identical there is a 7ms difference in GPU time.
This is fully reproducible purely through these traces. It's nothing to do with battery level, GPU temperature, or anything else I can find - I can literally switch back and forth 'Analysing' each trace on the same device, and the slow trace will always be slow and the fast trace will always be fast.
You can see a huge discrepancy in the very first draw call: a simple screen-filling quad. Same shader, same textures, same blend mode - same everything, so far as I can tell - yet it takes around twice as long (both vertex and fragment shader) in one trace as in the other.
Notes: Yes, our engine spits out some redundant GL calls. They're the same in both traces, though, so aren't relevant. All I'm trying to figure out is why sometimes the GPU time doubles to 14ms for a while, when nothing significant is changing.