It is not ... but ... (correct structure)

You are asking about how to express a logical relationship in a way that is unambiguously clear. You are right that there is a kind of clash between the singular noun and the two (and so plural) noun complements.

I would say myself that in the original sentence there is a presumption in favour your intended meaning: "is not 'X' but '(X and Z)'.

But that presumption does not remove the dissonance or the possibility of misunderstanding.
In the expression there is or ought to be a rule that where we are dealing with legal, scientific, technical or logical matters, precision trumps brevity and elegance. So say exactly what you mean. I do not think the single quotes will do that job.

So I would suggest that you have to say "Y and Z together", or "Y together with Z"; or, perhaps better still, "a <or 'the'> combination of Y and Z".

The factor that prevents data from altering is not 'X' but the combination of 'Y' and 'Z'.