We blithely convert stuff to money rather than sorting out the trades and get A sells food buys minerals, B sells food buys production, C sells production buys minerals. This works in terms of money, but of course we've just invented the minerals from nowhere, and sold more food than anyone wanted to buy! (this is a danger in any setup that isn't precisely balanced, i.e. every combination)
I think the problem we've had in this discussion so far is really an inability to agree upon the parameters of an economic model. For example, if this game were a market simulater (any of the Tycoon type games or games like Machiavelli, Merchant Prince, etc...) then the level of focus on the mechanics of trade mentioned above would be welcome, necassary and appropriate. However, this is a 4x game - the player is going to be focusing on diplomacy, warfare, exploration, etc, etc... Making the player spend this amount of attention on trade mechanics seems a little excessive.
A simple model where money represents an abstraction of the economics undoubtedly going on within and between empires can cover all of the game's needs without requiring an economics major or accountant to determine the optimal trade patterns for maximum profit.
One alternative, properly netting off the surplusses and deficits and then trading them between planets rapidly leads you into headaches trying to model the correct prices of commodities when modelling the market economy, just ask Krikkitone, he and EntropyAvatar bashed their heads against this one for ages.
The other, hamstringing the conversion process with strange rules, limits and ad-hoc arrangements, makes the players life so complicated you'd be much better off just keeping the resources completely separate and handling the surplus and shortfalls by independant allocation rules.
I would argue that money should represent an abstraction of economic activity tied to an arbitrary value rather than have it be tied to a specific resource. To tie money to production is the equivalent of using a "gold standard". If we keep money unfettered to production or any other resource, we can essentially have a floating value currency whose availability can be tied to empire size and level of development.
I look forward to seeing where all this economic discussion actually leads.
Oh yeah, for our younger members, the gold standard was when the dollar was backed by our federal gold reserves. Each dollar bill was redeemable for a specific weight of gold bullion.