We have similar problem witht the new creator which seems to have more checking. That is a good thing, however, it would be better if Cypress supply more information. or have app notes to explain what those warnings are and how to fix it. I think the quickest way for now is to issue a support case and have Cypress support to fix it.
The hold time violation is STA warning(Static timing analysis). You can learn more about how to understand the STA warnings and how to debug them, launch the PSoC Creator Help Topics and search for Static Timing Analysis.
I got a response from a FAE:
it seems that creator got in a digital routing loop that it couldn't get out. the answer is to delete the SPI component, and drag another copy back into the schematic.......