I'm not familiar with this book, but I looked at the draft second edition which is free at Taylor's web site here.
Section 7.3, equation (15) is
$$Δt_\text{rain} = γ_\text{rel}(Δt_\text{shell} - v_\text{rel} Δy_\text{shell})$$
I think your question is why the right hand side isn't just $γ_\text{rel} Δt_\text{shell}$. The reason is that the usual time dilation formula $Δt' = γΔt$ is, in effect, the Lorentz transformation equation with $Δx=0$. But here, the stone is stationary in the primed (rain) frame and moving in the unprimed (shell) frame, not the other way around. Also, $Δt, Δx, Δy$ here describe the motion of an arbitrary object, not necessarily the stone. ($v_\text{rel}$ is always the speed of the stone.)
If $Δt, Δx, Δy$ do describe the motion of the stone, then it would be correct to write $Δt_\text{shell} = γ_\text{rel} Δt_\text{rain}$ (note the reversal of the shell and rain labels), and you could derive the same result from that (using the fact that $v_\text{rel} = Δy_\text{shell}/Δt_\text{shell}$). You could also start with $Δt_\text{rain} = \sqrt{Δt_\text{shell}^2 - Δy_\text{shell}^2}$.
When $Δt=0$ then $Δy=0$ also (the object can't have moved, unless it's tachyonic), so their equation does give $Δt_\text{rain}=0$.
This derivation of Gullstrand-Painlevé coordinates is unique to this book (or at least unusual), and I find it confusing, in part because $Δt_\text{rain}$, despite its name, is not the Gullstrand-Painlevé "rain" time coordinate, which they later call $T$. The usual approach would be to just write $T=t+f(r)$, where $t$ and $r$ are the Schwarzschild coordinates, and solve for $f$ subject to the constraint that $T$ is the proper time of the stones. In this approach you never define any Lorentzian "shell" or "rain" frames.