Good point. And there may well be other ways that "junk" genes are metabolically expensive. For instance real genes probably aren't perfectly nonfunctional. Maybe they make the transcription or expression of other genes more (or less) costly, or they use up energy and materials being occasionally transcribed into nonfunctional bits of RNA or protein, or bind some factors, or who knows what else. And then selection can act on that.

But the scale just seems too small for any of that matter in most cases - because it has to matter at the scale of a single base pair, because that's the size of a mutation and point mutations can be conserved or lost independently of one another.

What is the metabolic cost (per cell per second) scale or order of magnitude where natural selection begins to operate?