question about supplying gas via multiple lines to a water heater
The first thing to ask yourself is this: do you want this solution to work, or do you want the job "done right?" The builder doesn't have to tear out the 1/2" line -- it could be abandoned in place. He would have to install a new section of properly-sized tubing, though. Consider whether you're willing to deal the logistics of that. It'll require cutting access holes through the drywall probably at the top and bottom of a wall in each level of the house and possibly some ceiling holes too. After the new tubing is installed all those openings will have to be repaired and the finishes blended. The contractor may begrudge being forced to do the work and, depending on his integrity, may not willingly give it his best.

The parallel pipes solution definitely feels weird even if it is functional. If you have doubts about this fix you can call in your local building official. If he rejects the work then that's that -- it'll have to be fixed or they'll revoke the occupancy permit for the house. Clearly that puts strong leverage on the builder to make the repair. You could also check with the technical service department of the manufacturer of the gas tubing.

There is a way to make the 1/2" tubing work: increase the gas pressure. You didn't mention which type of gas you're using nor in which country you're located, but I'll presume natural gas and USA. Natural gas appliances are generally designed for 1/4 PSI inlet pressure and gas utilities normally install a 1/4 PSI regulator at their meter. However, the gas utility could install a higher-pressure regulator - likely 2 PSI. Your builder could then install 1/4 PSI regulators inside the house. There could be one at each appliance or appliance group, for example. Be aware that the gas utility may charge a higher monthly "base charge" on your bill. In my area it costs about US$5/month more to have a 2 PSI service instead of a 1/4 PSI service.