| CFLAGS are set for optimisations. Whilst it is true that setting the wrong CFLAGS can cause your system to not work at all, not setting any CFLAGS will result in a working system.
Stage 3 is for those users who just want to set CFLAGS and install the system. You can use Genkernel to build your kernel whatever stage you used for installation - it's just a tool to make building the kernel much easier.
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