All,
The fabs will make anything you want. If you want a 5V IO, that is what you get.
The market (and here I mean where the money is) wants very fast DDR3 interfaces. To do this one requires 180nm IO transistors (optimally), or 250nm IO transistors.
That means 1.8v IO or 2.5v IO.
So, for a FPGA, one must choose the highest performance you need, and that will constrain your highest voltage options (unless you decide to have more than one oxide for IO, which greatly increases cost, and design complexity, decisions as to what to provide, and thus time to market).
So, Xilinx doesn't decide to 'drop' 3.3v. The V6 doesn't support 3.3v IO like in previous families, but S6 does. The customers told us quite clearly what was required, for their dollars (yen, NT$, euros, pounds, etc.).
As for 'safety margin' it is true that more aggressive process means perhaps less tolerance to overshoot and undershoot. Hopefully, the recommended operating levels in the specifications are clear, and good signal engineering practices are followed. If you don't care about SI, then you are likely to have other problems, so it isn't such a big deal anymore.
Austin