It's important to note two things. First, that the metal charts that are included in the books, and the appendices detailing them, are considered in-universe research. That is, this is what somebody out there thinks they know. Atium was included in the original metal charts simply because it was known. Many of the original assumptions about Allomancy were shaped around the Lord Ruler's witholding of information, the lack of knowledge about how the world was really created, and the lack of technology to do much more
than smelt and mix common ores.
That said, the second thing to note is that all we have is a single letter written by a new God to an old friend. Despite what we know, it's open to interpretation.
Following that, someone asked a question phrased differently, but received an answer that practically fits your question like a glove. From a long Q&A archive posted on Google, dated three days after Hero of Ages was released, I dug this out:
Are there any Allomantic metals we have not seen yet, besides Chromium and Nicrosil?
RAFO. (Sorry.) Let's just say that when Sazed said there are two metals you haven't found, he MIGHT not have been referring to a metal and its alloy, but two base metals. Who knows. Gods can be frustratingly ambiguous in times like that.
The Coppermind wiki entry on Allomancy also acknowledges this, stating in it's section on Development, that once Atium was officially off the charts by being revealed as a piece of divine power, Sanderson replaced it with cadmium and it's relative bendalloy. It unfortunately lacks a citation, and it doesn't make clear whether this was an evolution that Sanderson made to arrange his magic system better or whether it was intended all along, and I've been unable to find the original source on my own.
So unless I can dig up something else, by the Q&A statement, Sanderson intended Sazed's letter to be lightly ambiguous, and he could be referring to two new base metals, or just the two new powers that weren't based on time.