CPLD as a pass through (Input pin directly goes to Output pin) good or bad idea?

Hi,

The use of the clock tree will only be critical when you are running very high speed. Sometimes the QII will failed fitter due to user not using the dedicated clock tree but I remembered that we can always use altclktrl to move them to the clock tree.

Also it is not necessary all the time to use clock tree. In your case, I don't think you will need any dedicated clock pin. As mentioned by dwh, you can just run at slower SPI data rate.