Yes I was also confused by this.I definitely agree with your assessment. 'Contradict' was too strong a word, but I do think it was rather odd how the wording for the article made it seem almost mandatory when the S-IIIs received the same bone enhancement as the S-IIs (albeit differently) and the S-IVs have three different bone strengthening measures that I believe would make their bones close to the preceding Spartans. But you do raise a good point about their muscle enhancements.
I've rationalised it by thinking that 'virtually unbreakable' is a catch all term to mean very durable. Also we do know that the three Spartan generations are not equal when it comes to the potency of their augmentations, so this coupled with Armory Amore's article is evidence that the three Spartan generations do not have the same degree of bone strength.
While I agree that the bone augmentation of the Spartan 4s does sound impressive, remember that the Spartan 4s also receive more muscular augmentations than the previous generation and yet are still weaker than them.
The Spartan 4s receive muscular injections, muscle grafting and a material that allows their muscles to exert more force without damaging itself, in comparaison a Spartan 3 only receives the muscular density drug.
At the end of the day there isn't anything that directly contradicts the article, so until this changes we are stuck with this.
S-IIIs specifically makes me raise an eyebrow, as it was always my impression that Nylund strongly inferred that the S-IIIs were as potent as their forebears. He went as far as to say that their augmentations were "a quantum leap over the S-II's".
The position of a Spartan 3 relative to a Spartan 2 has always been a very ambiguous thing.
Ghost of Onyx never directly stated that the Spartan 3s had worst augmentations, and in fact the novel does have several moments that acknowledges the capabilities of the Spartan 3s such as them tearing the Covenant apart in CQC, Kurt calling Gamma the finest Spartans ever, more advanced augmentations.
However the fact that Spartan 3s were disposable shock troops that died in the hundred, coupled with their shorter size and less than ideal genes gave the community the impression that they were cheap knockoffs of the real thing.
It wasn't until Armory Amore, Glasslands, New Blood, and the Official Spartan Field Manual that we got a more concrete answer regarding their standing.
I do agree however that the articles words it very strangely.