I always wondered this as well. I've posted another thread out there regarding the extract kit instructions on why they don't have an option for those that want to perform full boils with an extract kit. Although how did you do all-grain batches - what size kettle?
I think most are okay if the water is doesn't have known contaminants or bacteria. If you have city water - it's chlorinated but that is a bad thing in terms of brewing beer. Well water alone can be safe without treatment but then again you have risk of something being present although many newer well water systems have UV, Osmosis...etc. There is a natural mountain spring close to where I live but it comes out of a iron rusted pipe. Haven't gotten a water test done on it. It's pure but that doesn't mean it's bacteria free either.
As to the 2-3 gal boil vs 6+....If I knew that the chances of contamination are almost nil....then I would do partial boils....but it just worries me - especially when you have to wait 20-30 days to find out if something went wrong. I would prefer to do 2-3 gal boils only because 99.9% of the extract kits out there have instrucitons based on that boil amount but now that I have a 8 gal kettle - I'll be doing full boils and I'll have to mess around with the hop utilization. I'm not a hop-head so I'm NOT going to add the hops per the instructions and make it hoppier than I want it because I used 6 gal or so for the boil. I guess it doesn't matter on the volume of water for the specialty grains? Making it too sweet because it steeped longer in 5 gal in getting the temp up to 170 vs getting 2-3 gal up to 170?