However, if you were to replace the rightmost resistor with another
cell, this time with an EMF of 6V and a negligible internal
resistance
In these kind of problems, it's best to explicitly include the internal resistance in the calculation and then see if, in fact, one can neglect the internal resistance of both voltage sources.
(However, such a circuit is no long a parallel circuit unless one does a source transformation of each voltage source with series internal resistance to a current source with parallel internal resistance.)
In that case, the voltage across the center resistor is easily found by superposition:
$$V_R = \frac{R||r_2}{r_1 + R||r_2}5\, \mathrm{V} + \frac{R||r_1}{r_2 + R||r_1}6\,\mathrm{V}$$
where $r_1$ is the internal resistance of the $5\,\mathrm{V}$ source and $r_2$ is the internal resistance of the $6\,\mathrm{V}$ source.
Now note that setting either $r_1 = 0$ or $r_2 = 0$ is OK for the voltage calculation. For example, setting $r_1 = 0$ yields
$$V_R = 5\,\mathrm{V}$$
The current out of the $6\,\mathrm{V}$ source is then
$$I_2 = \frac{6 - 5}{r_2}\, \mathrm{A}$$
and the current out of the $5\,\mathrm{V}$ source is thus
$$I_1 = \frac{5}{R} - I_2\, \mathrm{A}$$
We see that, for $r_2 \le \frac{R}{5}$, the current $I_1$ is negative, i.e., the $6\, \mathrm{V}$ source supplies power to the $5\, \mathrm{V}$ source.
But note that we cannot now set $r_2 = 0$ since, as $r_2 \rightarrow 0$, the current $I_2 \rightarrow \infty$.
So, in fact, you can't meaningfully stipulate that both voltage sources have negligible internal resistance.
It's interesting to also consider the case that $r_2 = k\cdot r_1$ and then let $r_1 \rightarrow 0$. You then find that
$$V_R \rightarrow \frac{k}{1 + k}5\, \mathrm{V} + \frac{1}{1+k}6\, \mathrm{V}$$
and
$$I_1 \rightarrow - I_2 \rightarrow \infty $$