If the mod is an update, that won't work, because you need files from the old mod and the new mod.
If the mod is a new version of the old file then your way works just fine.
oh i see sorry, your talking about installing part of the mod via NMM just using the changed/updated files, thought you were talking about installing a whole new version of the mod. Which is what i do, if there is a update, to save things from getting messy i just download the whole new version of the mod and do my method, unless its a 1gb+ texture pack where i would download the update and let it overwrite whatever.
Sorry, i misunderstood the question.