Here is a (very...) hand-made approach that becomes conjectural at its end.
I will use just $y$ for $y(x)$, the functional dependence being understood.
We start by the premise that $\forall x \in(0,\infty)$
$$y: y> 0 \quad {\rm and}\quad y' = xy-1. \tag{1}$$
we want to know whether $(1)$ implies
$$y''y-(y')^2 \geq 0 \implies y'' \geq \frac{(y')^2}{y}. \tag {2}$$
Differentiating $(1)$ we get
$$y'' = y + xy'\tag{3}$$
Combining with $(2)$ we require
$$ y + xy' \geq \frac{(y')^2}{y} \implies y^2 + xyy' -(y')^2 \geq 0. \tag{4}$$
Using $(1)$ we essentially require
$$y^2 + xyy' -(y')^2 = y^2 + (y'+1)y' -(y')^2 = y^2 + y' \geq 0.$$
This will obviously hold if $y'\geq 0$.
We next examine what happens if/when $y'<0$.
For this case it holds
$$y'< \implies x < \frac 1y \implies xy' > \frac {y'}{y} \implies y+ xy' > y + \frac {y'}{y}$$
$$\implies y'' > \frac {y^2+y'}{y}.\tag{5}$$
This holds. So to prove that a solution $y$ while $y'<0$ is log convex , it is sufficient (but not necessary) to show that, combining $(5)$ and $(2)$,
$$\frac {y^2+y'}{y} \geq \frac{(y')^2}{y} \implies y^2+y' \geq (y')^2 \implies y^2 \geq y'\cdot (y' -1)$$
or show that
$$y^2 \geq (xy-1)(xy-2) = y^2(x-1/y)(x-2/y)$$
or
$$1 \geq \left(x - \frac 1y\right)\left(x-\frac 2y\right).$$
Re-arranging this as a $2$nd degree polynomial in $x$ we require
$$x^2 - \frac 3y x + \left(\frac 2{y^2} -1\right) \leq 0,$$
so we require that $x$ lies in the interval in between the roots of this polynomial, which are
$$x_{1,2} = \frac{3\pm\sqrt{1+4y^2}}{2y}$$
and one can verify that
$$\frac{3-\sqrt{1+4y^2}}{2y} < \frac 1y < \frac{3+\sqrt{1+4y^2}}{2y}.$$
What we just proved is that for a $(x,y): y'<0$, $y$ will be log-convex for
$$\frac{3-\sqrt{1+4y^2}}{2y} \leq x < \frac 1 y$$
and we still need to prove what happens for $0< x < \frac{3-\sqrt{1+4y^2}}{2y}$, which is a feasible inequality as long as $y < \sqrt{2}$ (needed for the upper bound to be strictly positive). Because we do not know what $y$ is, to cover all cases, we consider the case that this inequality holds. So we are left to examine the log-convexity of the solution $y$ for
$$y: y'<0, \quad y< \sqrt{2},\quad 0<x < \frac 1y g_1,\; g_1\equiv \frac{3-\sqrt{1+4y^2}}{2} < 1.$$
There is a reason why we defined $g_1$. Because now we can re-start the process that led to eq. $(5)$,
$$x < \frac 1y g_1 \implies xy' > \frac {y'}{y}g_1...$$
and arrive at the sufficient condition for log-convexity
$$1 \geq \left(x - \frac 1y\right)\left(x-\frac {1+g_1}{y}\right),$$
consider the new $2$nd degree polynomial in $x$ etc, which results in shrinking even more the range of $x$ for which log-convexity is not yet proved... so I conjecture that, a bit like fixed-point convergence, iterating this should eventually cover all values of $x$, and fully prove what the OP was wondering about.