The Big Ben has multiple (6) WC outs - I'd probably use them in that fashion.

I'm not knowledgeable with MADI itself - but I believe BNC WC is recommended over embedded MADI or ADAT WC.  There are likely some cases where it won't make any discernable difference (like say 3 ADI-8's on a Digiface - the ADI-8's would use BNC to lock to each other - but the Digiface could gladly use ADAT Reference w/o any ill effects)

I doubt the actual ASIO latency would be any different depending on the PCIe slot you use.  Some have even claimed that the sound quality is different from PCIe x1 off the MCH/ICH versus a PCIe 16x off the CPU, but I find that concept highly amusing myself .