As noted in the comments, both methods potentially break down. Kepler's method is mathematically exact, but as formulated here it becomes ill-conditioned as the eccentricity approaches 1. The mean and eccentric anomalies become undefined for a parabolic orbit because a parabola lacks a center. Numerov's/Cowell's method approximates the propagator with a Taylor series whose accuracy is not guaranteed for eccentricities all the way up to a limiting value of 1.
To separate these issues we should put Kepler's method into a form that remains well-conditioned all the way to the parabolic limit. This proper conditioning will then guarantee the accuracy of the Kepler result, against which the Numerov/Cowell result can be compared.
In this discussion the time from periapsis is used together with the anomaly conversions given below, the latter taken from Wikipedia:
$t=\sqrt{\dfrac{\alpha^3}{\mu}}M=\sqrt{\dfrac{r_p^3}{(1-e)^3\mu}}M \tag{1}\label{Eq 1}$
$M=E-e\sin E\tag{2}\label{Eq 2}$
$E=2\tan^{-1}\left(\sqrt{\dfrac{1-e}{1+e}}\tan\dfrac{\theta}{2}\right)\tag{3}\label{Eq 3}$
In Eq. 1 $r_p$ is the periapsis distance, which unlike the semi major axis remains bounded and well-defined all the way up to (and beyond) eccentricity $1$.
When $E$ is calculated from $\theta$ via Eq. 3 with $e$ approaching 1, we get $E$ proportional to $(1-e)^{1/2}$; but in order to have finite and bounded times the mean anomaly $M$ must be proportional to $(1-e)^{3/2}$. Therefore Eq. 2 which connects $M$ to $E$ is ill-conditioned, for we are inputting terms with the lower power proportionality to get a difference with the higher-power proportionality.
To get $M$ in terms of quantities having the proper proportionality for a well-conditioned operation, render
$M=E-e\sin E = (E-\sin E)+(1-e)\sin E = ((\sin^{-1}s)-s)+(1-e)s$
where $s=\sin E$. This equation holds for $|E|\le\pi/2$ corresponding to $\theta\le 2\tan^{-1}(\sqrt{(1+e)/(1-e))}$. For larger true anomalies we can use Eqs. 1-3 directly because the ill-conditioning does not arise. Hereafter we focus on the case $\theta\le 2\tan^{-1}(\sqrt{(1+e)/(1-e))}$.
From Eq. 3 and the trigonometric identity $\sin(2\tan^{-1}u)=2u/(1+u^2)$ we obtain
$s=\dfrac{2\sqrt{\dfrac{1-e}{1+e}}\tan\dfrac{\theta}{2}}{1+\dfrac{1-e}{1+e}\tan^2\dfrac{\theta}{2}}\tag{4}\label{Eq 4}$
Now we have to tackle $\sin^{-1}s-s$ which is proportional to $s^3$ whereas the terms are proportional to $s$. To eliminate this ill-conditioning, convert this transcendental function to an integral involving an algebraic one:
$\displaystyle{(\sin^{-1}s)-s=\int_0^s\left(\dfrac{1}{\sqrt{1-x^2}}-1\right) dx = \int_0^s\left(\dfrac{x^2}{\sqrt{1-x^2}(\sqrt{1-x^2}+1)}\right) dx\tag{5}\label{Eq 5}}$
We have invoked the difference of squares factorization to rationalize the numerator, which gets rid on the ill-conditioned subtraction. This may be integrated numerically to obtain a well-conditioned result at high eccentricity. Since the integration is independent of the orbit, values as a function of $s$ may be stored beforehand in a table for lookup.
Put this all together and we obtain the time from periapsis for a highly eccentric orbit from a modified version of Eq. 1:
$\displaystyle{t=\sqrt{\dfrac{r_p^3}{\mu}}\left(\dfrac{1}{(1-e)^{3/2}}\int_0^s\left(\dfrac{x^2}{\sqrt{1-x^2}(\sqrt{1-x^2}+1)}\right) dx+\dfrac{s}{(1-e)^{1/2}}\right)}\tag{6}\label{Eq 6}$
with $s$ determined from Eq. 4.