first of all, kudos on your effort to break a photography problem down to first principles.
The discrepancy you've observed stems from a common oversimplification. Your 100mm Lens is actually what optical engineers refer to as a "lens assembly" As you likely know, it is comprised of multiple lens elements in groups working in tandem to form, refine, and transmit the image seen by your imaging sensor.
If your 100mm lens assembly consisted of a single 100mm lens element you would have massive distortions and only red, green, or blue could be in focus at a time but the thin lens magnification equation you'd linked would hold true. Magnification of 1 would be achieved when the subject is 200mm from the nodal point and the lens assembly would need to be physically greater than 200mm in length. Even then, this would only be strictly accurate to the extent which the thin lens equation is appropriate (and it is not particularly appropriate here.) A proper answer would come from a derivation of the lensmaker's equation
A corollary of the difference between an assembly and a lensthin lens is bilocated nodal points. A lensthin lens has a single location for both the front and rear nodal points.points; Both are collocated with the entrance pupil. If this were true of your lens assembly you would be able to free-lens by rotation around your lens' aperture without any parallax to the subject or sensor. I'm sure if you tried this with the 100mm macro you would find that its not true. A thick lens has two nodal points which are only collocated if its net index is 0, I.E. it has no focal length. A lens assembly can be approximated by a virtual thick lens with two idealized indices such that the virtual lens has the same vertices, relative focal lengths, entrance pupil, and (saliently) nodal points as the lens assembly.
For extra credit, you could check the description of a compound lens and try to guess which combinations of lens focal lengths would create the situation you've described. NB the "telescope magnification." This is essentially what a lens designer does.
For additional reading you can check out the different types of photographic lens designs