Sounds kinda boneheaded to me. It's a stretch, but the only rationale I can come up with for doing that is that the owners requested that it be done that way so the gameroom and the one bedroom upstairs could be at the same temp as the lower level. The only way that I can conceive of where that would make sense was if the other upstairs rooms weren't planned to be used heavily (and the gameroom and bedroom were) and they wanted to avoid running the entire upstairs system.
That said, it's not likely to work well. Unless there's a separate return upstairs, it's always going to be warmer up there just due to simple physics: hot air rises; cold air sinks. Even with a separate return, it's a questionable approach, especially if there is any opening to the other areas upstairs.

Is there a chance that the physical design of the home precluded running ducts easily from the 2nd floor system to those areas, and the main floor system was used since ducts from there could be snaked into the area?