How to determine the hydroxide ion concentration in an acidic aqueous solution?
The problem that you are facing comes from the fact that technically, not all of the $\ce {OH-}$ reacts with the $\ce {H+}$.  It is only because the amount of OH- that doesn't react is so negligible compared to the amount that does, that the $\ce {[H_3O+]}$ can be taken to be $\ce{[HCl]-[$\ce{OH-}$]}$.

So, yes, to find the remaining (negligible) amount of $\ce{OH-}$, you must use the "very small value" given by either subtracting $\ce {pH}$ from $14 =\ce{pOH}$ or doing $\ce K_w/[\ce{H+}]=[\ce{OH-}]$ (which amounts to the same thing).