(the story was that it was a Chinese subcontractor. Remember that SuperMicro is a Taiwanese company; I'm pretty sure that SuperMicro has less Chinese made content than any of the other major manufacturers of commodity server kit. )
I did know people cutting open power supplies, cutting open capacitors (a place chips have been hidden in the past) and otherwise examining the systems at the macro level.
I also knew people who managed networks of these things... and one of the bloomburg stories, as I recall, claimed that the hack was discovered via looking at the network as the BMC tried to phone home.
I mean, yes, you could do something more clever than that, replace a chip with one that looks identical, which uses the same traces that did something different, but the article certainly implied it was a more simple sort of thing.
I mean, if I was trying to compromise a BMC in that way, I'd just flash it with firmware that did what I needed (and this has happened before... to many different vendors) - my understanding of the bloomburg story was that there was some bit of hardware to re-flash the firmware to the compromised version after the user upgraded to a non-compromised version.