Various beam shaping approaches were examined to counter the negative influence of surface aberration arising when inscribing optical waveguides deeply inside of glass with a femtosecond laser. Aberration correction was found unable to completely recover the low-loss waveguide properties, prompting a comprehensive examination of waveguides formed with focused Gaussian-Bessel beams. Diverging conical phase fronts are presented as a hybrid means of partial aberration correction to improve insertion loss and a new, to the best of our knowledge, means of asymmetric beam shaping. In this way, low-loss waveguides are presented over shallow to deep writing depth (2.8 mm) where morphological and modal properties could be further tuned with conical phase front.