Thanks for bringing it up with the developers :smileyhappy:
We set it on the VMDK itself since we want to limit MB/s. SIOC v2 with the IO filter only has IOPS setting which makes it unpredictable in regards of throughput due to changing IO size, at least that's my experience with it.
The need for throttling comes from using dedupe volumes on our storage array (3PAR). The storage array is not able to keep up and the cache runs full making the whole array crawl. I've logged a case with HPE in regards of that since I was hoping it would protect its cache better. The bottleneck there actually appears to be CPU and not disk performance.