Building a higher end workstation, why actually not using an ATX-mobo in place of an mATX?
Right, the case would be a little larger.
So, the decision, concerning the mobo, is to go for a GA-Z87-HD3. The advantage, very obviously, is having a lot of expansion possibilities.
The idea of using Fractal Design's DEFINE mini hast to be ditched consequently. However, the "DEFINE mini" is just the smallest of the "DEFINE" silent computing cases. Here, the decision is to obtain a DEFINE R4. Since Apple decided "black" was the new "white" (cf. new Mac pro), the choice is obvious, in particular since the black DEFINE R4 looks the best of the bunch.