1000 gallons @70% yield = 70% total product x 100% take = profits on 70% product
vs.
1000 gallons @99% yield = 99% total product x 35% take = profits on 34.65% product (so just from those 1000 gallons they make half as much money)
I don't understand why greater purity = greater yield. It should be the opposite. The less pure it is, the more filler there is. It's an inferior product, but they should end up with more of it.That's not to say they can't make more money selling the pure stuff. They can definitely charge a higher price for it.
In any case, your comparison above isn't apples-to-apples. Without Heisenberg, they have to pay their own cooks and acquire their own raw materials. With Heisenberg, they're getting a 35% cut on the yield from 1,000 gallons of methylamine that they don't have to acquire elsewhere. (They do have to pay Mike $5 million for his 333 gallons, but they're getting a cut of the other 667 gallons, apparently worth $10 million as methylamine but worth hundreds of millions when converted to Heisenberg's meth, without having to pay for it.)