I understand your confusion; the wording of this message should more properly refer to 'clk', and not 'clk_enable'.
Your design appears to have three clock rates: the base rate (determined by the master clock), along with rates 2x and 4x slower than the base clock. The slower rates are implemented by feeding each generated FF with the master clock and a clock enable that runs at the appropriate multiple of the base clock. HDL Coder auto-generates a timing controller to drive these enables.
The base rate will be whatever clock you feed to your device. The slower rates in your design will be 2x and 4x slower; controlled by the local clock enables driven by the timing controller.
