I think yes, for me it would an improvement. The only bad thing here is my lack of the ideas on how to implement such forking.
We already do it for user.reg vs system.reg, though in this case it's separate registry "hives". I'm not sure if we can do it on the key level.
I'm certainly not bothered by this, and I think when people realise they hardly ever have to configure Wine it'll all blow over, but if somebody else wants to do the patch be my guest ...