You are concerned that it is not synchronized on the input?
Based on the picture, the output of the lookup table is synchronized.
If you are already synchronizing the input with a FF as your picture and question at the end of your post seems to indicate, then using the same clock for the FF's that is used for clocking the lookup table would synchronize the input and output of the lookup table to change at the same time for changing the lookup value.
If any of the signals coming in through the Smart I/O Component terminals are meant to be used in sequential elements in the LUTs, the terminal synchronizer must first be used to synchronize that signal to the Component clock. If the signal on gpio0 must be used in LUT0 in Sequential output mode, the synchronization for gpio0 terminal should be enabled for reliable operation.