Many of these non-coding areas are actually enhancer elements. These elements produce enhancer RNA, previously thought to be noise, and regulate distant genes thanks to chromosome conformation. Chromosome conformation means DNA folds in complex 3D patterns.
The interplay between chromosome conformation, enhancer RNA, gene expression and disease variants is very complex and interesting [1,2].
I know some startups trying to regulate genes by targeting enhancer elements. The field is very promising, but a big roadblock seems to be to deliver compounds to the right cell type.
Junk DNA was always contentious because there was evidence of conservation in these areas. In other words, evolution was selecting against mutations in some junk DNA regions. My impression is that junk DNA fell quickly out of favor once the ENCODE Project started to publish large scale epigenetics data in the early 2010s.
[1] https://genomebiology.biomedcentral.com/articles/10.1186/s13...