My guess is that cc is a broken compiler on many exotic operating system (or at least was when the ./configure was first written in the nineties), and in particular does not support the (modest) gcc extensions that the runtime relies on. Using a standardized (yet portable) compiler was deemed an easier path to configure the OCaml distribution build system than trying to support the oddities of every Unix's C compiler under the sun.
Note that the compiler distribution builds just fine under MacOS, which now uses Clang (llvm) instead of GCC -- and that you can configure the C compiler you want to use with (./configure -cc ...). I don't see what is the problem here; and I would think that opting to choose GCC by default is still a perfectly reasonable choice today.