Re: "Just because something mechanically fits, doesn't mean that it will actually work." We're learning that for FMC! 8-} (It wasn't an issue in the relatively small HSMC land). Interesting, we looked at a TI DaughterCard and they chose to use the M2C/C2M signals despite the spec for these signals as "multi-gigabit transceiver data pairs." so yes, every one takes their own path.
Anyway - after doing a "bake off" of Zynq vs. Altera, we decided to stay with the Arria V SoC card due to some advantages, and build a little interdiction routing card to handle the 8 problem signals.
Thanks guys - this has been educational for sure!
/j