Couple of things:
When transitivity says that if $xRy$ and $yRz$ implies $xRz$, please note that $x$, $y$, and $z$ do not need to be 3 different objects. For example, we could pick $x=1$, $y=2$, and $z=1$. Or we could pick $x=y=z=3$.
So, actually there are $x$, $y$, and $z$ such that $xRy$ and $yRz$: for example, when $x=y=z=3$, we have $xRy$ and $yRz$, and so for transitivity to hold, we do need to verify that we have $xRz$, but with $x=z=3$, that holds too, so we're good.
Also: even if there would not be any $x$, $y$, and $z$ such that $xRy$ and $yRz$, you can still have transitivity. In fact, you must have transitivity in such a case! Consider the 'empty' relation $R = \{ \}$. Well, this $R$ is trivially (or 'vacuously') transitive, because it is true that if we ever have $x$, $y$, and $z$ such that $xRy$ and $yRz$, then we have $xRz$ as well. That is: for all of the zero (!) cases where we have $xRy$ and $yRz$, we have $xRz$ as well ... and so we're good!
Put differently: for transitivity not to hold, we must have some $x$, $y$, and $z$ such that $xRy$ and $yRz$, but not $xRz$. But with this empty $R$, we never have $xRy$ and $yRz$, and so we certainly don't have $xRy$ and $yRz$, but not $xRz$. So again, transitivity holds.