As this appears to be the OPs own design, there really aren't any deviations from standard. This house IS the standard. It is a matter for the OP to fit in what they want within the budget, and there will almost always be some tweaking here and there to ensure that it works.
I agree. There is no harm in asking.
But there is a builders standard. Flat ceilings with either truss or stick constructed hip and valley roof is the standard.
As I said, in reality different construction methods may not cost a great deal more however most mainstream builders will slug you for deviating from their standards. You may strike a builder who is prepared to build for the real cost but installing highlight windows in a skillion roof is more expensive and difficult from a construction point of view, so the OP should be prepared to pay for this.
It would definitely be cheaper to redesign the house now so as to take advantage of passive solar design principals while maintaining relatively standard building practises, than to try and retro build in methods to overcome design failings.