There is evidence even from the early days of genomics that recombination and thus evolution worked in (approximate) units at a time. This means that when a new mechanism for regulation appeared, it often regulated many pathways coded in idiosyncratic ways. That leads to the observed local commonality of mechanism.

The place that I saw this in my own work was in the way that ends of intervening sequence (introns) was coded for excision during expression of proteins. The different ends of different introns behaved differently and introns in different parts of genomes had slightly different dialects.

The relationship of similarity and locality in regulators is different from this, but is another case of proximity being a proxy for similarity.