We establish the existence and uniqueness of pathwise strong solutions to the stochastic 3D primitive equations with only horizontal viscosity and diffusivity driven by transport noise on a cylindrical domain $M=(-h,0) \times G$, $G\subset \mathbb{R}^2$ bounded and smooth, with the physical Dirichlet boundary conditions on the lateral part of the boundary. Compared to the deterministic case where the uniqueness of $z$-weak solutions holds in $L^2$, more regular initial data are necessary to establish uniqueness in the anisotropic space $H^1_z L^2_{xy}$ so that the existence of local pathwise solutions can be deduced from the Gyöngy-Krylov theorem. Global existence is established using the logarithmic Sobolev embedding, the stochastic Gronwall lemma and an iterated stopping time argument.