The volume pot in my S2 Mira was not the same as the Alphas in my SE, and it definitely was not the Core-spec CTS. It was an unmarked, unidentifiable piece that went bad very quickly - I'd say within the first 2-3 months it already sounded weird and basically Sh_t the bed after 6 months. Mine too had the awful taper when new, which the Alphas don't seem to have.
I replaced it with a Gibson Historic pot that I had in my toolbox (they are CTS), which dropped right in, no reaming necessary. The Gibson pot is very firm, much more so than the CTS pots that PRS uses in the core guitars, but I like that feel personally and I use the volume pot a lot. Has an awesome taper as well.
The tone pot looks identical to the core-spec pot that PRS sells in their web store but I couldn't tell if you if it is actually the same. I have had no issues with it though. The feel of the two is dramatically different - the CTS/Gibson one is very firm and feels almost damped while the stock tone pot turns very easily (too easily IMO). I don't care about the different, but you may.