I am sure Specialized bikes are well made, and of quality. You are right, it's not just about the version of the Shimano components being used.
However, Trek bikes seem to be well made too (at least the one I have seen and tried), so I have no specific reasons to pay more for a Specialized.
I do want a hybrid bike: I don't want a road bike (don't like the position), and I don't want a mountain bike (too slow).
I am riding 30% on the road, 30% on tow paths along the Thames, and 30% in parks.
I am not commuting with the bike, and typically only use it when the weather is dry, so I don't believe I need disk brakes either. They are heavier, and more difficult to maintain/fix. They also make the wheels a lot more difficult to remove. Since I won't be riding at high speed, or going down mountains, I don't think I need the breaking power either.
If I was commuting to work everyday on a bike, then I fully agree that disk brakes would be preferable.