In order to achieve the servicability and fault tolerance that server buyers demand, servers like the PowerEdge 2500 have quite a few proprietary components that wouldn't be compatible with an off-the-shelf motherboard. And that's assuming that you can get a different motherboard to fit inside the case at all, much less in a way that allows the cooling and expansion slots to line up properly.
It would be cheaper and easier to buy a case designed for the motherboard you want.