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You're referring to regulatory regions which really represent a tiny component of the genome (in terms of base fraction)... but nobody has really constructed a strong argument (that can be tested) that long stretches of Alu (which comprise most of the junk DNA) actually have a regulatory or other function.

It's speculated those regions are gene foundries, but it's mostly speculation with limited evidence.

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I think there's a 'balancing game' between "I need my DNA to be as compact as possible" (no waste of energy, faster to duplicate, less chance for errors) and "I need space in my DNA to allow new things to evolve".

In zebrafish and mouse, the more "developmental" a gene is, the more SPACE it seems to have around it. More space means more regulation and more potential for new regulation.

That's a fine hypothesis, but proving it is near impossible.

I thought they were part of the structural mechanisms of the regulatory regions, ie they need long stretches of dna to facilitate it looping regulators back onto the allele

That's a hypothesis, but not one with enough support to be considered true.

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