Is this (genes physically close together, but not contiguous, being affected by the same/related promoters) something commonly seen? I'd love to learn more about it if so!
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.