If you simply put the line into ext-miscdests-custom it will actually appear just where the include line is; but since the Noop line is exactly that, a No-Op line, the effect will be the same as if it had appeared where you show it.
It is an extremely risky business to modify extensions.conf and extensions_additional.conf manually, because then you have to remember to make that change everytime you update to a new release of FreePBx. So where it is not necessary, like here, don’t do it.
If there were actually a line after the include which does something, the easiest way would be to simply duplicate all relevant lines from ext-miscdests in ext-miscdests-custom as well, then the entire call gets handled there and in the right order. Better than modifying extensions_additional.conf.