As you say, you are proving that $f: \langle x,y \rangle \mapsto \langle \text{gcd}(x,y), \text{lcm}(x, y) \rangle$ is associative.
I'll write $g: \mathbb{N}^n \to \mathbb{N}$ for the GCD function, and $l: \mathbb{N}^n \to \mathbb{N}$ for the LCM, using the handy convention of $g(a,b,c)$ for $g(g(a,b),c)$ etc - justified by the next paragraph.
I claim first that $g$ is associative. Indeed, that's obvious just by considering the prime factorisations of the inputs. Likewise $l$, although you could prove this by using $l(x, y) = \frac{x y}{g(x, y)}$.
Now, I claim that $g(l(x, y), z) = l(g(x,z), g(y, z))$. This again follows by considering the prime factorisations.
Therefore, it is possible in any expression of the form "sequence of LCMs and GCDs" to pull out all the LCM terms to the front. Moreover, the resulting expression is precisely of the form $l( g(a,b,\dots), g(c,d,\dots), \dots)$ with no further levels of nesting. We just need to prove that the structure is the same however we apply the operations.
In your example, {4, 6, 9}, we find {g(4, 6), l(4, 6), 9}, then {g(4, 6), g(l(4, 6), 9), l(l(4, 6), 9)} which is $$\{g(4, 6), l(g(4, 9), g(6, 9)), l(4, 6, 9)\}$$
Finally, $\{g(g(4,6), l(g(4,9),g(6,9))), l(g(4,6), l(g(4,9),g(6,9))), l(4,6,9)\}$ which is $$\{g(4, 6, 9), l(g(4,6), g(4,9), g(6,9)), l(4,6,9)\}$$
This is manifestly symmetric, so it can't matter which order we took the operations in to get there.
I didn't rely on any special properties of 4, 6, 9: they stand in for general $a, b, c$. It's clear, by the way, that we need to stop the procedure here, because $g(a,b,c)$ divides $l(g(a,b),g(b,c),g(a,c))$ which divides $l(a,b,c)$.
This generalises, messily, by induction.