  We analyse hypercharge flux GUT breaking in F-theory/Type IIB GUT models with
regards to its implications for anomaly cancellation and gauge coupling
unification. To this aim we exploit the Type IIB limit and consider 7-brane
configurations that for the first time are guaranteed to exhibit net
hypercharge flux restriction to matter curves. We show that local F-theory
models with anomalies of type U(1)_Y-U(1)^2 in the massless spectrum can be
consistent only if such additional U(1)s are globally geometrically massive (in
the sense that they arise from non-Kahler deformations of the Calabi-Yau
four-fold). Further, in such cases of geometrically massive U(1)s hypercharge
flux can induce new anomalies of type U(1)_Y^2-U(1) in the massless spectrum,
violating constraints in local models forbidding such anomalies. In particular
this implies that it is possible to construct models exhibiting a U(1)_{PQ}
global symmetry which have hypercharge flux doublet-triplet splitting and no
further exotics. We also show that the known hypercharge flux induced splitting
of the gauge couplings in IIB models at tree-level can be reduced by a factor
of 5 by employing a more F-theoretic twisting of U(1) flux by hypercharge flux
bringing it to well within MSSM 2-loop results. In the case of net restriction
of hypercharge flux to matter curves this tree-level splitting becomes more
involved, is tied to the vacuum expectation values of certain closed-string
fields, and therefore gauge coupling unification becomes tied to the question
of moduli stabilisation.
