It is demonstrated that ultrafast laser writing in silica glass depends on the grade of silica glass associated with the method of its manufacture. Moreover, laser-written modifications, in particular birefringent modifications, reveal a dependence on the geometry of writing, that is, the modification strength of voxels is smaller than that of single line structures and multi-line scanned areas, which can be explained by free carrier diffusion and reduced electric field in scanning writing. The retardance of scanned birefringent region produced in the regime of anisotropic nanopores formation in silica glass manufactured by vapor axial deposition (VAD) is about five times higher than that in an electrically fused sample at the same laser writing parameters, while the difference in retardance of a nanograting based modification in synthetic and fused silica is only about 10%. The phenomenon is interpreted in terms of the higher concentration of oxygen deficient centers in the electrically fused silica glass, which can confine self-trapped holes and prevent the nanopores formation. Improvement of high transmission optical elements is demonstrated in the VAD sample, and low cost multiplexed optical data storage with higher capacity and readout accuracy is realized in the electrically fused silica glass.