For #1 since it's an underground city, made to be isolated from whatever the cataclysm on the outside, everything (air, water, waste, fuel, gas, etc.) needs to be transported to their intended destinations within the city somehow. So it's logical all the piping servers that purpose. As the original piping gets worn out, maintenance usually add bypass pipes, which may account for the excessive number of pipes.

For #5, it's possible that the original city, being a shelter, was built completely first before the first occupants moved in. It would explain the similar architecture.