Looked into this a bit more. While a misaligned partition does show slower performance in a benchmark, the difference is not that big. So it shouldn't be a big issue in real-world usage. Getting partitions aligned is still a good idea though. Reducing write/erase cycles helps extend the lifespan of the SD card.
For more benchmark numbers with other cards, check these threads:
http://androidforums.com/threads/samsung-evo-micro-sd-feel-as-fast-as-internal.890591/
http://androidforums.com/threads/sandisk-32gb-extreme-plus-uhs-1-u3-sd-card-review-test.893742/
Looking at the numbers, I think SanDisk Ultra seems to be a capable card and I don't think the performance of the card is a big concern. But this is just my opinion.
@aangbell I have another thought. Have you changed some performance settings after installing and using the hack, like overclocking, governor, scheduler, etc.? I am not sure about this, but those could be settings that are read and applied before the hack is active, as I mentioned in the usage notes. They might have an effect on performance difference with the hack and without the hack.