It's a very subtle issue I can't go fully into here. I agree with a lot of your concerns. Personally I would usually go for cost-welfare analysis rather than cost-benefit analysis, which resolves many of the problems you're concerned about.
In terms of behaviour change, giving a mixed message is just going to excuse people falling back into the default method. This is what thoughtless acceptance of the default means:
http://www.heritage.org/environment/report/discounting-clima... http://www.heritage.org/government-regulation/report/questio...
So I think there's a real cost and risk associated with not taking a clear position on this.