Apple has had a "fix" for the lag since as far back as July last year. They implemented it into the Webkit rendering engine via the nightly channel.
But... for whatever reason (likely because they were working on 10.9), they decided not to implement that version of Webkit into Safari, and instead opted to just do minor bug fixes.
1 year later, 10.9 is upon us, and does contain the "fix".
So it is a software problem that Apple chose to ignore.
Source: Fact.
Even if you force the 650M to be on constantly in OSX, it still lags the same way given the right circumstances. The 650M is even faster than Iris (and Iris Pro), so the logical conclusion is that the GPU is not at fault.
Is the CPU at fault? Nope. Both the 13" rMBP and 15" rMBP lag the very same way. So at this point, the only conclusion is that the problem is not hardware-related.