Hi Maiden,
Since the controller is not a bridge spanning-tree typically isn't necessary.As well, most contemporary switches support PVST+ or other spanning-tree modes, where the controller only supports 802.1d. The conflicts between these spanning-tree modes would be unresolvable unless the switch were to be reconfigured to do 802.1d, if it could and as we know it is not possible.
Bypassing the issue tends to be easier and more stable. Enabling it could cause potential problems, or cause the root switches to believe that the controller will behave like a conventional switch, when it is not doing so.
HTH
Ankur
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