Cycles per byte is pretty standard for crypto algorithms, and tends to give consistent results across an architecture. It is usually measured with dynamic frequency scaling disabled.

Do you have a source for use of AVX2 automatically reducing clock frequency? I found this:

"Because Intel AVX instructions generally consume more power, frequency reductions can occur to keep the processor operating within TDP limits. [...] Performance of workloads optimized for Intel AVX instructions can be significantly greater than workloads that do not use Intel AVX instructions even when the processor is operating at a slightly lower frequency"

Which seems to indicate that it would only trigger when you're doing a fair amount of work with it, which should be giving you a total performance benefit.