Hi Dave,
I definitely agree on it not being completely fleshed out. I had a fair amount of pain myself using it in Stratix IV. I recall the .ipx issue as well and wasn't too pleased that SIV was left unsupported. Now that I'm in AVGZ, I'm finally getting to take advantage of the improvements.
For AVGZ, I'm using the low latency PHY for hardware eval. In this case, I pretty much gutted the example design. The loopback and pattern generator/checker (with bypass) pieces are working for me. I believe Native PHY is supported for the toolkit directly as well. I've attached my qsys system as a txt file in case you're interested.
Scott