Look at Eckert and co-worker's study on Y aluminborate glass compositions and particularly the discussion of REDOR results.(1)

In general, I would imagine that the relative stability of the two species you identified ([4]Al-O-[3]B and [4]B-O-[3]B) might be dependent on composition. I suspect concentration, size and charge of the modifier oxide and Al/B ratio would be important to consider. Eckert and co-workers also did some studies in aluminoborate glasses and showed that [4]B-O-[3]B avoidance is seen to a greater extent when the cation field strength is lower, but the results differed slightly for two series with different MO:Al2O3:B2O3.(2) There is a also lot of research in different compositional regions about estimating structural deviations from a random model or [4]X-O-[4]X avoidance model. I'll just reference a very recent publication from the Stebbins lab here, but feel free to message for a bunch of earlier literature.(3) Additionally, how good the modifier is at stabilizing [4]B-O-[4]B versus [3]B-NBO depends on the size and charge of the cation (i.e. see borate research papers (4) and (5)). 

References

(1) Deters, Heinz, Andrea SS de Camargo, Cristiane N. Santos, Cynthia R. Ferrari, Antonio C. Hernandes, Alain Ibanez, Matthias T. Rinke, and Hellmut Eckert. "Structural characterization of rare-earth doped yttrium aluminoborate laser glasses using solid state NMR." The Journal of Physical Chemistry C 113.36 (2009): 16216-16225.http://pubs.acs.org/doi/abs/10.1021/jp9032904

(2) Chan, Jerry CC, Marko Bertmer, and Hellmut Eckert. "Site Connectivities in amorphous materials studied by double-resonance NMR of quadrupolar nuclei: high-resolution 11B↔ 27Al spectroscopy of aluminoborate glasses." Journal of the American Chemical Society 121.22 (1999): 5238-5248. http://pubs.acs.org/doi/abs/10.1021/ja983385i

(3) LaComb, Michelle, David Rice, and Jonathan F. Stebbins. "Network oxygen sites in calcium aluminoborosilicate glasses: Results from 17 O {27 Al} and 17 O {11 B} double resonance NMR." Journal of Non-Crystalline Solids 447 (2016): 248-254.

http://pubs.acs.org/doi/abs/10.1021/ja983385i

(4) Michaelis, Vladimir K., Pedro M. Aguiar, and Scott Kroeker. "Probing alkali coordination environments in alkali borate glasses by multinuclear magnetic resonance." Journal of Non-Crystalline Solids 353.26 (2007): 2582-2590.

http://www.sciencedirect.com/science/article/pii/S0022309307004073

(5) Wu, Jingshi, and Jonathan F. Stebbins. "Cation field strength effects on boron coordination in binary borate glasses." Journal of the American Ceramic Society 97.9 (2014): 2794-2801. http://onlinelibrary.wiley.com/doi/10.1111/jace.13100/full

http://pubs.acs.org/doi/abs/10.1021/ja983385i

Thanks for the detailed response, Elizabeth.

-Ashutosh