This article seems to argue that Nature has selected for genes (and by extension, perhaps whole genomes) that in some sense are likely to benefit from small mutations.
That means that even if two genomes lead to phenotypically identical organisms, the one whose genome is more robust to small changes (either by continuing to function the same way, or to have a different, but still useful function) is better.
Is there a specific term for this? This implies that 'How likely is this particular organism to survive in this particular environment?' is not precisely the same as 'How well will this genome persist over evolutionary time as the environment changes?', but they seem to both go under the term 'fitness', even though one is more 'meta-' than the other.
Similarly, software engineers do not simply search the space of programs for ones that give the exact desired output, but within the set of working programs that identical output, we also select for ones where small changes will lead to different but still-useful programs. We call these features 'maintainability' and 'readability', and we use 'libraries' to help do this.
And just like we don't necessarily use the entirety of a library, it seems possible that large stretches of non-coding DNA are simply genes that aren't currently useful, but are kept around as raw material for future evolution.
"It is not the strongest of the species
that survives, nor the most intelligent;
it is the one most adaptable to change."