I often have to recompile the kernel because the Digi RealPort port server drivers don't like the distribution kernel. In any case, the RealPort drivers want the compile set on the machine for their install.

I also have often had to recompile for special equipment - these are industrial machines, not home computers. I do not know what will be needed in the future, so I am not comfortable shipping a machine that is not ready and tested for recompile.
Recompiling with my own .config also removes heaps and piles of unneeded stuff.

Besides that, my clients insist on mounting FAT media in various ways, and Debian has the wrong character set as default.