Okay, so MIDI clock is a specific tempo format, and like I said, live musicians don’t necessarily stay exactly on time, some tracks change their tempo throughout a track, or during a breakdown, or a chorus, etc. Traktor doesn’t reflect this kind of fluctuation in how it treats a track, because for nearly all electronic music, much of hip hop, and even a lot of modern studio “mixed” rock and pop, the beats per minute tempo will not change throughout a track, because its either been composed electronically or altered in production to stay at exact tempo.
You shouldn’t need to turn sync on and off while playing a track, personally, I leave it on, unless I am mixing into something that specifically necessitates there being no automatic beat-matching between tracks (mixing a 160bpm drum n bass track into the textural intro of a trip hop track that’s around 90bpm or something like that).
MIDI clock from Traktor is in effect sending a message to Maschine that says “I am at X BPM” and when you allow the MIDI clock from Traktor to control Maschine, it will play at the that tempo. It doesn’t just sort of send the tempo, it iron-fisted controls the tempo.
However, if your beat grid is off, if your song playing shifts tempo, if the samples you are using in Maschine are not correctly chopped for changing tempo (for instance, if you have a 1 bar long sample, its only ever a bar long at the tempo it was recorded at, so if the master tempo from traktor is 98, and your 1 bar sample in maschine is 92bpm, nothing can make it 98, but it will trigger on the measure its been recorded to. This isn’t an issue if your Maschine project is built up of kick drum hits, horn stabs, percussion hits, and so on, because those just continue to be played on the measure, and the length doesn’t matter as much, most of the time).
The scene retriggering works nearly exactly the same as cue points in Traktor, in that it waits for the next closest exact beat to start playing, although in Maschine you can choose if you want it to start on an 1/8th, 1/4, or just start again at the end of the scene. Traktor’s cue points (with quantize and sync both turned on) will start at the next beat grid division in the phrase (it tries to match the downbeat, rather than just hit the next note, whereas Maschine will hit the next note, quarter note, eighth note, etc), this also means that as the tempo of the track goes up Traktor seems to trigger cue points more quickly, but this is only because a faster track has a “smaller” beatgrid, you just get to the next downbeat in less time.
So, leave sync on. Use Scenes in Maschine. Don’t trigger long samples in Maschine and expect them to match different tempos from Traktor, and don’t expect old soul and disco tracks to stay on the same tempo thru the whole track, and set smart beat grids when you’re going to be using those tracks alongside anything that you’re going to be using in a set where you send out master clock to other devices.