$\newcommand{\tb}{\tilde b}$Let us write $b,t,x,k$ instead of $|\lambda|,x,y,r$, respectively, so that for real $t\ge0$
\begin{equation*}
x''(t)+V(t)x(t)=0, \tag{-1}
\end{equation*}
where
\begin{equation*}
V(t):=b^2+g(t),\quad g(t):=\frac{k e^{-t}}{(1+e^{-t})^2}. \tag{0}
\end{equation*}
Let us show that for all real $t\ge0$ and $k\ge0$ we have
\begin{equation*}
|x(t)|\le C(b)(|x(0)|+|x'(0)|), \tag{1}
\end{equation*}
where $C(b)>0$ is a real number depending only on $b>0$.
If $|x(0)|+|x'(0)|=0$, then $x(t)=0$ for all $t\ge0$, so that (1) is trivial. So, without loss of generality $x(0)\ge0$, and $x'(0)>0$ if $x(0)=0$.
Then, by Theorem1 (used with $a=0$ and $b_*=b$, since $V(t)\ge b^2$), for the smallest positive zero $t_1$ of $x$ we have
\begin{equation}
t_1\le\pi/b<\infty. \tag{2}
\end{equation}
It is now clear that the roots $t_j$ of $x$ in $(0,\infty)$ form a strictly increasing sequence: $t_1<t_2<\cdots$. Moreover, by (-1) and (0), $x$ is concave on each of the intervals $[0,t_1], [t_2,t_3],\dots$ and convex on each of the intervals $[t_1,t_2], [t_3,t_4],\dots$.
By inequality (13) of the mentioned paper, we have
\begin{equation*}
|x(t)|\le\sqrt{x(0)^2+x'(0)^2/b^2} \tag{1a}
\end{equation*}
for $t\in[0,t_1]$ if $x'(0)>0$, whence (1) holds.
On the other hand, if $x'(0)\le0$ (while of course $x(0)\ge0$), then, by the concavity of $x$ on $[0,t_1]$, $x$ is decreasing on $[0,t_1]$ from $x(0)$ to $0$, so that (1) is trivial in this case. Thus, (1) holds on $[0,t_1]$ in any case.
Inequalities (2) and (1a) were based on the trivial estimate $V(t)\ge b^2$, which can be improved for $t\in[0,t_1]$ to
$$V(t)\ge b^2+ke^{-t}/4\ge b^2+ke^{-t_1}/4\ge b^2+ke^{-\pi/b}/4=:\tb^2,$$
in view of (2), with $\tb\ge0$.
Next, by (-1), (0), and (1a) with $\tb$ in place of $b$, $|x''(t)|\le(b^2+k)\sqrt{x(0)^2+x'(0)^2/\tb^2}$.
If now $x'(0)>0$, then $x'(s)=0$ for some $s\in[0,t_1]$, and hence, in view of (2) with $\tb$ in place of $b$,
\begin{equation*}
|x'(t_1)|\le(b^2+k)\sqrt{x(0)^2+x'(0)^2/\tb^2}\,\pi/\tb\le C_1(b)(|x(0)|+|x'(0)|), \tag{3}
\end{equation*}
where $C_1(b)>0$ is a real number depending only on $b$.
Similarly to (1a), for $t\in[t_1,t_2]$ we get $|x(t)|\le\sqrt{x(t_1)^2+x'(t_1)^2/b^2}$;
but $x(t_1)=0$; so, for $t\in[t_1,t_2]$
\begin{equation*}
|x(t)|\le|x'(t_1)|/b\le C(b)(|x(0)|+|x'(0)|) \tag{4}
\end{equation*}
by (3), where $C(b):=C_1(b)/b\in(0,\infty)$, so that $C(b)$ depends only on $b$.
Similarly to (4), for all natural $j$ and all
$t\in[t_j,t_{j+1}]$ we get $|x(t)|\le|x'(t_j)|/b$.
So, it remains to show that $|x'(t_{j+1})|\le|x'(t_j)|$ for all natural $j$. In turn, in view of (-1) and because $g(t)$ is nonincreasing in $t\ge0$, inequality $|x'(t_j)|\ge|x'(t_{j+1})|$ immediately follows from
Lemma 1: Suppose that $f\colon[0,1]\to\mathbb R$ is concave and twice differentiable, $f(0)=f(1)=0$, and we have the implication
\begin{equation*}
0\le s<t\le1\ \&\ f(s)=f(t)\implies f''(s)\le f''(t).
\end{equation*}
Then $0\le -f'(1)\le f'(0)$.
It remains to prove this lemma.