First: your claim about $k[x,y,z,w]/(xz - yw)$ being $k[x,z]$ is not quite correct. We would have $k[x,y,z,w]/(y,w)\cong k[x,z],$ or even that $k[x,y,z,w]/(x - y, z - w)\cong k[x,z].$ However, when forming $k[x,y,z,w]/(xz - yw),$ you have the relation that $xz = yw,$ which you can't split up into the two relations $x = y$ and $z = w.$ In fact, there cannot be any abstract isomorphism between $k[x,y,z,w]/(xz - yw)$ and $k[x,z]:$ $k[x,z]$ is a UFD, but $k[x,y,z,w]/(xz - yw)$ is not!
Now, as you noted, irreducibility of your first two polynomials is equivalent: we can define an automorphism of $k[x,y,z,w]$ by
\begin{align*}
\varphi : k[x,y,z,w]&\to k[y,w,x,z] = k[x,y,z,w]\\
x&\mapsto y,\\
y&\mapsto w,\\
w&\mapsto z,\\
z&\mapsto x.
\end{align*}
Applying $\varphi$ to $xw - y^2$ gives $$\varphi(xw - y^2) = \varphi(x)\varphi(w) - \varphi(y)^2 = yz - w^2.$$ Therefore, the first polynomial is irreducible if and only if the second is.
To actually show irreducibility, I would not try to compute these quotients explicitly. Instead, I'd apply the generalized Eisenstein's criterion.
For $xw - y^2,$ we may write $k[x,y,z,w] = k[x,z,w][y].$ Then if $\mathfrak{p} = (x),$ it is clear that $\mathfrak{p}$ is a prime ideal in $k[x,z,w],$ and moreover that $xw\in\mathfrak{p},$ but $xw\not\in\mathfrak{p}^2 = (x^2).$ Thus, $-y^2 + xw$ satisfies Eisenstein's criterion for $\mathfrak{p} = (x),$ and is irreducible.
You can play the same game with $xz - yw:$ again write $k[x,y,z,w] = k[x,z,w][y],$ and again let $\mathfrak{p} = (x).$ $\mathfrak{p}$ is still prime, and $xz\not\in\mathfrak{p}^2 = (x^2).$ Thus, $xz - yw$ is irreducible.
Notice that nowhere did I assume anything about the characteristic of $k$! The above holds for all fields.