I can see this working in two different ways:
The first way is: What if, instead of 2 different, equally-sized metals, if instead you had the ability to combine metals with valuable gemstones which have been specially treated with elemental properties, and in the process create metals with unusual properties? That way, it doesn't seem silly because the gems themselves would be destroyed in the process, and you might have a hefty chance of failure even at upper levels of skill, but the end result incase of success would be something really interesting. This would require a new Elementalist skill, and dwarves would only be able to create certain gems they'd have an affinity for, like for instance ones for elemental Earth, Fire, Salt, Magma, etc. Others (ice, storm, time, acid, whatever) would have to be purchased from other races. This would allow you to create substances with different useful properties-Elemental salt weapons might be useful against undead, for instance, whereas obviously fire weapons could set things on fire (including your stuff). Weapons, themselves, would still function as their base metal and quality would indicate, in addition to the elemental property.
The risk would be that failure might result in releasing the angry trapped elemental creature into your fortress.
The second way is to expand the Alchemy skill, to allow very skilled alchemists to enhance, rather than alter, the properties of your metals by researching and creating alloys. This would entail purchasing or creating expensive and volatile chemicals, and be an elaborate process, rather than simply shoving two different metal bars into each other. You could, in this way, create a metal that would be of a better quality than it's base (more suitable specifically for weapons or armor or other applications), or lighter, or more valuable. The downside would be that the more involved the alchemic process, the greater and wider level of miasma it would cause, as a result of pollution.