That's true of protein coding sequence, but things are a little bit more difficult for regulatory DNA because

1)Regulatory DNA is under MUCH less sequence constraint - the relevant binding proteins are not individually fussy about their binding sites

2)Regulatory Networks have a lot of redundancy

3)Regulatory Mutations can be much more easily compensated for by other mutations - because we're dealing with analog networks, rather than strings of amino acids.

Regulatory evolution is an immature field but it seems that an awful lot of change can occur in a short time. The literature is full of sequences that have an experimentally provable activity (put them on a plasmid with a reporter gene and off it goes) and yet show no conservation between species. There's probably a lot more functional sequence that won't just work on it's own on a plasmid, or show a noticable effect from knockouts. It may be that regulatory networks are composed of a continous distribution from a few constrained elements with strong effects down to lots of unconstrained weak ones. The latter will be very, very difficult to distinguish from Junk DNA.