I've only designed one Arabic font yet and don't actually read any of its languages, so I'm probably not the right person to ask.
But isn't your base glyph + diacritics idea already the status quo in modern type design apps such as Glyphs? (For Latin as well.) Sure, some formats unlink the components in a compound glyph during export, but that's probably for backward compatibility with "dumb" user applications.
As for your deconstruction of linked glyph variants, I think that would only work for extremely geometric typefaces that forego the rich texture of traditional Arabic script. The small irregularities in the practical realization of a character's underlying design in initial, medial, final, isolated, and even ligated environments add to the legibility of a typeface; they are not dead weight.
Since you name-tagged me: I haven't done any commissioned work so far, so I wouldn't know. In the case of the Cormorant family, the «negotiations» basically came down to Dave Crossland making an offer and me going «OMG how much...?!».