There is a lower algorithmic computation factor to the Animation codec versus something like ProRes. ProRes requires a fair amount of CPU power where Animation requires little. This is why your renders are faster with the Animation codec.
If your adding a clip out of AE for FCP *and* you intend on further stacking layers to that AE clip in FCP (e.g., adding text and such on top of it), then I would absolutely render out of AE using an RGB[A] 4:4:4: lossless codec, like Animation, PNG, SheerVideo or Microcosm. This is so your AE clip maintains its RGB lossless quality on the timeline and allows FCP to perform the final Y'CrCb color space compression at the very last step.
With that in mind, it doesn't matter which hardware you want to use. If you're trying to decide between Kona 3 and HDio, I'd choose based on editing workflow needs rather than rendering needs.