I would say that it depends on how literally you take the word "always". e.g., If you've got a regex that is so simple as to need no explanation, I would say that including /x, but no internal whitespace/comments, is cargo cult because the /x has no effect. /m and /s are similarly pointless to include when dealing with data which is known to not contain newlines.

I'm always skeptical when I encounter the phrase "best practice". (In my experience, it tends to mean "We think this is the right thing to do, but can't be bothered (or aren't able) to explain why.") In this particular case, using /xsm with /(\d{3})-(\d{4})/ makes about as much sense as preferring $foo =~ /^bar$/xsm over $foo eq 'bar'. KISS. If you don't need the extra power/complexity, don't take special measures to make it available.