If each note sung triggers that notes diatonic chord (on a vocoder) - and the notes are all in key- then will those chords ever clash with the chords of the instrumental or will they always be in harmony with the instrumental - like octaves and the perfect 5th, 4ths etc.
Short answer: no.
That always depends on when the note is sung, for how much time, how the vocoder is programmed and the harmonic context (including the musical style).
Let's ignore the last aspect for now and assume that we're only talking about triads.
In a major tonality, you'll have:
- good results while singing the tonic and (usually) the third degree
- fine results (depending on the situation) with the sixth
- similar with the dominant
- ambiguous results singing the leading tone
- possibly clashing with the second and, more importantly, the fourth (which is usually considered an off-limits note even without its harmonization)
In a minor (natural) tonality:
- good results with the first, third, and fifth degree
- fine results with the seventh
- ambiguous results with the sixth
- fourth and second depend on the situation
Consider that: I'm not exploring other minor tonalities, and this is a major simplification.
That said, as with any diatonic note (and off-key note), that depends on when you sing it and for how long.
If the tonic of the given chord is not the key of the piece, the actual result of the above may vary, even dramatically.
If it's played off-beat or for a short (or not meaningful) time within the extent of the harmony, it might be ok, or even interesting.
As always, use your ears, do experiments, and also remember that, while it's common practice to have the harmonizing follow the chords of the song, it doesn't mean that you have to strictly and always follow them.
Restricting yourself to the chords of the key doesn't prevent clashes (depending on exactly what you think is a 'clash'). For example, you might reasonably sing B over a C major chord, but the sound of a B diminished chord and a C chord simultaneously is likely to sound somewhat dissonant.
The best starting point is probably to drive the vocoder with the chords of the song.
It can work, but it often doesn't. And it's not always passing notes that are the problem. They are a problem, as they're often included in a bar where there's one chord only. Harmonising with passing notes will produce more, different chords/harmonies. Not what the song needs.
Then there's notes sung which are still in the diatonics, but the harmony for that part may be out of the key. For example, in key C, a bar with note D may need a D/D7 harmony to lead to the next bar of G - a modulation, say. I that D bar, the harmony would go for note F, whereas F♯ was needed. Not good.