I think you raise some very interesting points @loke , and points with which I agree:
The price-ratio that you get from Mercere is probably the worst one available, but it has the benefit that you can always use it. The Mercere are always willing to supply any amount of vis, of any art, assuming you can pay. (It is tempting to raise counter arguments like "can the Mercere really raise any amount? but remember that the limit is that the players have to be able to pay.)
I also think that the rates charged by the Mercere are so exorbitant that they are never used by anyone except the truly desperate and those who need so large amounts of vis that they can negotiate for better rates.
You can problably get better rates if you are willing to wait and have a specific conversion in mind. E.g. if you only ever want to convert 4 Animal vis to as much Auram vis as possible then you have the luxury of seeking out a specific environment with a favorable conversion rate for just this specific conversion, and can afford to not bother with the wider market. E.g. making friends with a local Animal-vis hungry magus who has an abundance of Auram vis, and then you can make a specific favorable agreement that would not be available in a broader market context.
If you find yourself in this situation the broader state of the market doesnt matter.
This may sound far fetched but most magi dont really need "generic" vis rather they tend to need specific amounts of specific types of vis. Often with a marked preference for certain types. This leads to lots of situations where individual magi often find themselves in non-generic situations and are able to exploit the fact that their individual needs dont line up with what the market expects.
I think it is worth mentioning that while not all vis is consumed equally, it is likely that the supply of in-demand vis is higher than for less demanded vis, because magi are a lot more likely to seek out sources of e.g. Vim, Corpus and Creo vis, than they are sources of e.g. Aquam vis. Thus sources of "useful" vis are more likely to be discovered, and creatures that yield "useful" vis are more likely to be hunted than those that yield less useful vis.
I do think that bookkeeping with generic vis is a useful tool that magi likely use in managing their accounts. I think in practise settling accounts in whatever types of vis are available to those settling accounts. I imagine that often bulk debts are settled primarily in whatever types of vis are abundant locally. In practise it might happen something like "covenant A owes 20 vis to Covenant B and when it comes time to pay they offer 20 of the locally abundant Aquam vis. Covenant B demands that the payment be done in more useful types as they need vis for ongoing projects, none of which are Aquam related. In the end they reach an agreement for a payment of 6 Vim vis and 14 Aquam vis." In all likelihood the 14 Aquam vis will be passed on to another less than happy victim later on and so the cycle continues.