Combining matrix transformations

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So I know that matrix multiplication is not commutative. And yet, I am taught that transformation matrices can be composed to arrive at a single transformation. So then, suppose that I have 3 matrices - each representing a rotation about each axis of a 3D coordinate system. How can I be sure that I arrive at the correct result, if the order matters?

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You are conflating two different things. Given two matrices $A,B$ it is true that the order in which list them before you multiply them matters in the generic case - you wouldn't expect $AB = BA$ to be true without further information. The technical statement of this is that matrix multiplication may not be commutative.

When you have 3 or more matrices we can talk about a different kind of "order". If you multiply the three matrices to get the product $ABC$ the question arises whether this means you multiply $A$ and $B$ to get another matrix $X$ and then multiply $X$ and $C$. Or should you multiply $B$ and $C$ to get another matrix $Y$ and then multiply $A$ and $Y$. The fact is, out of those two possibilities you always get the same result. It is in this sense that the "order doesn't matter" which you are talking about. The technical name for this is that matrix multiplication is associative.