OK, I'll be using Supermicro or intel workstation boards in the future. The models I have tested work with all the RAID controllers I have thrown at them. They support "above 4G PCI decoding", configurable "base mmcfg" value and downshift of PCI-e speed. This also makes them compatible with Quadro GPU's and Xeon Phi boards. They also tend to not have lane-switching IC's that seems to create noise on the PCIe busses. They have high quality power phases and they don't overclock the CPU(s) behind you back. Also the built in LAN adapters tend to be high quality.
Guess I won't be buying any Haswell-E cpu's or X99 boards. I'll just have to wait for the Xeon models to arrive.