Ok -here's what's going on
1) Altera does support Vita57.1 for FMC. However, your card is uses the "user-definable" pins. Altera did a somewhat arbitrary assignment of their (non-bidirectional) LVDS signals to these user-definable pins, and in some cases didn't match the direction used in your card. I think if you had used the M2C/C2M pins there would have been no problem. I haven't checked Xilinx docs, but based on your prior statement I assume it's no problem with Xilinx because their LVDS are bi-dir and so can deal with any config of those pins.
I'm still sort of screwed though, because we can't use your board with the card we want, and the Xilinx cards with their Zynq+large fabric (like the one you mention above) will take weeks to get :-(.
/j