SPI Interrupt Handler delay in STM32F303?
I have nothing on the timing difference, but I do have a possible workaround: if you are able to prepare your response frame in advance, use DMA to both send your frame and catch the transmitted frame.  I've found the DMA in the STM32F4 to be a bit fiddly to get going, but once you understand the sequence that you have to configure things in it works very well indeed.