  Supersymmetric flux compactification of F-theory in the geometric phase
yields numerous vacua, and provides an ensemble of low-energy effective
theories with different symmetry, matter multiplicity and Lagrangian
parameters. Theoretical tools have already been developed so that we can study
how the statistics of flux vacua depend on the choice of symmetry and some of
Lagrangian parameters. In this article, we estimate the fraction of i) vacua
that have a U(1) symmetry for spontaneous R-parity violation, and ii) those
that realise ideas which achieve hierarchical eigenvalues of the Yukawa
matrices. We also learn a lesson that the number of flux vacua is reduced very
much when the unbroken $U(1)_Y$ symmetry is obtained from a non-trivial
Mordell--Weil group, while it is not when $U(1)_Y$ is in SU(5) unification. It
also turns out that vacua with an approximate U(1) symmetry forms a locus of
accumulation points of the flux vacua distribution.
