Hi,
I think the answer is hidden in your question. You talk about "the meaningful musical onset of the note exactly on time".
The thing is that what is "musically meaningful" depends very heavily on the context. In some musical contexts it might be correct to say that you want the end of the attack phase exactly on the beat. In other musical contexts you might want the beginning of the attack phase on the beat. Yet another context might want the middle of the attack phase on beat.
So the musician or composer is the only person that can decide what the correct meaning is for their musical performance. And the only way in which they can do that is if synthesizers don't add meaning to the musical input, but simply execute the commands and leave "meaning" to the musician or composer. As soon as a synth forces meaning onto the input, you take away control from the musician.
So what you describe as a flaw - that synths ignore the meaning of the note onset of samples - is actually a feature. It gives musicians a consistent and predictable system that they can use to add meaning themselves.
Cheers
Marcus