When you pluck a guitar string, initially the vibration is chaotic and complex, but the components of the vibration that aren't eigenmodes die out over time due destructive interference
This is a misconception. The vibration is initially only as complex (or non-complex) as later during the tone†. The string moves the whole time according to some partial differential equation; it so happens that eigenmodes provide an efficient way of solving this PDE (because the PDE is to good approximation linear), but you can just as well look at it completely in time-domain. The string shape starts out as an asymmetric triangle (cf. Why do harmonics occur when you pluck a string?), then wobbles its way to the other side, then back. In the ideal case (infinitely thin perfectly elastic no air infinite-impedance end stops), it will then return exactly to the original shape. Rinse and repeat.
The string shape can at all times be described as a superposition of the harmonic eigenmodes, because these form a basis of the space of all possible shapes the string can have. But that doesn't really mean it "is" the superposition of these harmonics, you could also expand the shape in any other basis, such as Legendre- or Chebyshev polynomials. Only, these aren't eigenbaseis, and therefore you couldn't easily predict how the expansion evolves over time. The sense in which the shape "is" the expansion in sinusoidal harmonics in particular is that these are the overwhelmingly most convenient basis, so we choose it. Once we've chosen it, any talk about "non-harmonics" is meaningless – the harmonics are the only functions there are in our basis.‡
This post contains some animations that may illustrate the point.
†Actually it is true that the vibration gets simpler over time, but this has nothing to do with non-harmonics. Instead, it is because higher-frequency harmonics tend to get damped more quickly than low-frequency ones, so at the start you have many more harmonics contributing to the movement than later on. But they're still all harmonics.
‡If you added more functions to it, the system wouldn't be linearly independent anymore and therefore the expansion ambiguous. This has nothing to do with the physics of strings, it's just a matter of how the mathematics behind "expanding an element of a vector space in some basis" works.