CMakeLists: Move off of modifying CMAKE_*-related flags

Modifying CMAKE_* related flags directly applies those changes to every
single CMake target. This includes even the targets we have in the
externals directory.

So, if we ever increased our warning levels, or enabled particular ones,
or enabled any other compilation setting, then this would apply to
externals as well, which is often not desirable.

This makes our compilation flag setup less error prone by only applying
our settings to our targets and leaving the externals alone entirely.

This also means we don't end up clobbering any provided flags on the
command line either, allowing users to specifically use the flags they
want.