”This is much more likely related to gut microbia metabolism than it is to histidine”

Yes and no: the study linked to in the El Pais article suggests that certain bacteria are converting histidine to imidazole proprionate.

More histidine -> more food for those bacteria -> bacterial overgrowth, dysbiosis and increased ImP levels -> eventually atherosclerosis.

There are probably some microbe(s) capable of outcompeting the ImP-producing ones even in the presence of increased histidine, which would serve as a mitigating factor.