For most use cases I believe that option 2 is just as good as option 1. However, I can see a few situations in which one would want to do it manually.
A package maintainer wants to build separately as they want separate packages for mpfr et al.
Someone who wants to pass different configure arguments/CFLAGS to each of the packages.
A GCC developer who wants to keep their source and build trees small as they don't make any changes to MPFR/GMP/etc.
I haven't done too much work with the (rather ugly) GCC build system, but I haven't seen any obvious differences in how the binaries are built.
I'm not the biggest authority on this though, so YMMV; I may be wrong.