Its not ideal if you are running something that cant be virtualised. For example you have a big SQL server. The board goes and you replace it with another board. the chances are you will have to reinstall the os and it will take more time.
An excellent reason for using off-the-shelf parts - I can nip down the road to Maplins and get a motherboard, harddrive, etc, in under an hour, no problem - in four hours I reckon I could have an entire server built and ready to start running virtual machines.