For instance you can select up to 4 augmentation dots
I wouldn't consider this lacking in N3 but rather practical since the sure fire way to get dirty looks from musicians is to make them play more than a double dotted note. its sort of like using theoretical keys (Fb for instance). True in theory they exist, but to use them is probably not practical.
you can hide the numbers on tuplet runs
Same situation; This is one thing in Notions notation that DOES adhere to MOLA (Major Orchestral Librarian's Association). In a real life situation where people are trying to perform your music, hiding the number would most certainly just lead to confusion and with rehearsal time at a premium, this could prove disasterous.
is Da Capo and Dal Segno which arent available in Notion 3
I believe they are in N3, just look under the palette that has the repeat/barline.
Choosing key signatures is a lot easier (especially for those of us who cant remember which signature is five flats!)
Remember, Protege is intended to teach music composition to beginners (which I cannot see being a very good thing) who need a little help (remembering the circle of 5ths for instance

. Notion is intended for more hi-end/professional applications. So there is more assumed knowledge of music in general.
That being said...
I cannot see a reason to have both, I would just use N3.
just my 2cents