That explanation isn't accurate. Perl complains about using \1 in the right-hand side of a substitution because using $1 is preferred. Whether the script is entered on the command line or not isn't important.
#!perl -w
use diagnostics;
$_ = 'foo';
s/(.)/\1/;
This script produces the following output:
\1 better written as $1 at tmp.pl line 5 (#1)
(W) Outside of patterns, backreferences live on as variables. The
+ use
of backslashes is grandfathered on the right-hand side of a
substitution, but stylistically it's better to use the variable fo
+rm
because other Perl programmers will expect it, and it works better
if there are more than 9 backreferences.
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