Firstly, the entire colony does not need to be entirely of domes. Domes can be used for the living habitat for settlers, the forest, and for agriculture, where there needs to be an element of 'openness' and efficient supply of sun light. For industrial and storage units, simple match-box like structures with slanting sides can be used to save on material and simplify structure assembly -- any automatic, non-labor intensive units don't even need to covered with glass at
all! You can give it a continuous case like form. Glass is gonna be expensive.
The glass used on the dome should be composite. Research is being done on glasses that block out UV rays etc and are crack resistant. A typical glass panel for the dome should be made out of layers of such glass supported on a carbon fiber mesh. A metal wire should not be used as it may overheat and is denser. Bullet proof glass is a popular recommendation on these boards, but bullet proof glass- if my engineer uncle whom I discussed this topic with few years back is right - is not actually completely bullet proof; it shatters after a few shots and needs replacement. Moreover, a respectful meteor should have kinetic energy much higher than that of a bullet.
Also, the moon has no atmosphere, so you will have no atmospheric pressure acting on the dome. So the scene of maintaining 1 atm inside the dome will require extra strong structures will get complicated as a pressure which works for domes on Earth may cause a rupture on the moon. You can do the math and show that off.
I saw a discussion of Gamma Ray Bursts here. Large bursts are created during supernovae or when material is sucked into a blackhole when it is paired up in a binary system, I think. Our steller neighborhood is pretty safe in this case (contestable statement). Solar flares and Coronal Mass Ejections (CMEs) from the Sun can be significant problems, though. They can fry satellite circuitry. A powerful enough CME can evaporate Earth's atmosphere. CMEs are mostly random and not fully understood, but Solar Physicists are researching about the Sun's eleven year cycle and devise an early warning system. You could propose using this research to design your emergency operations and apparatus.
I think that the location will have a large implications on the design. I'll suggest locating near the poles. The most important reason is that near the poles, there is a large area of around 12000 square kilometer that remains dark all the time because of the tilt of the moon. Here, water brought by foreign bodies does not decompose and evaporate. Plus the poles have less caters.
Building in caters is complicated as it affects mobility of the machinery. The problem is further exacerbated by the low gravity. It will also severely limit your design options. It will also require you to carry out surveys to check the stability of the crater. E.g don't you think that the fringes of the craters created on impact can collapse - slide as they have side ways pressure acting
and lack material support on one side?
And about the underground tunnels, why do you need to go underground? It is sure a very tantalizing concept, but when the sun's out, the ground can heat up to several hundred degrees. If you don't dig really deep (do something inefficient and wasteful), the heat is gonna reach the tunnels and require extensive cooling systems and insulation. You can save the hassle by building surface tunnels and then cooling the ground/floor. You can argue that it will protect it from meteorites, but if the rest of your colony domes - the larger part of the colony - can get hit, why save just the tunnels that are mere supplements?
The regolith and dust depositing on the moon can be removed by pouring water from the top of the dome when the physicals conditions are such that water will be able to maintain a liquid state while flowing down the dome. You should mention when and how such conditions will be insured. The water then be collected at the bottom, filtered and reused. The residue dust can be removed and used. OR you could create a system that repels dust and prevents that from
settling. You can do this be ionizing the air around the domes such that any inward particles get a particular charge. You can then give the dome an opposite charge! Simple O level Physics, but research this before validating this crazy idea. You can increase the expanse of this layer to possibly repel charged particles from space too.
Also, I ran through the project presentation. I do not see any communication dishes. You'll need an array of dishes for high speed/bandwidth communication with the earth and a satellite network as you can have extended periods of radio blackouts near the poles, or any side when its not facing the earth. Look into virtual telescopes. Virtual telescoping techniques can enable you to create a virtual continent-sized dish and make your communication systems very powerful.