Effects of X-ray irradiation on the electronic structure of LaAlO$_3$/SrTiO$_3$ (LAO/STO) samples, grown at low oxygen pressure and post-annealed ex-situ till recovery of their stoichiometry, were investigated by soft-X-ray ARPES. The irradiation at low sample temperature below ~100K creates oxygen vacancies (VOs) injecting Ti t2g-electrons into the interfacial mobile electron system (MES). At this temperature the oxygen out-diffusion is suppressed, and the VOs are expected to appear mostly in the top STO layer. However, we observe a pronounced three-dimensional (3D) character of the X-ray generated MES in our samples, indicating its large extension into the STO depth, which contrasts to the purely two-dimensional (2D) character of the MES in standard stoichiometric LAO/STO samples. Based on self-interaction-corrected DFT calculations of the MES induced by VOs at the interface and in STO bulk, we discuss possible mechanisms of this puzzling three-dimensionality. They may involve VOs remnant in the deeper STO layers, photoconductivity-induced metallic states as well as more exotic mechanisms such as X-ray induced formation of Frenkel pairs.