What existing code could changing $ to use \R instead of \n potentially break? Could this raise security issues by widening input validation patterns?

A bit difficult to say, as even \n is not just a LF but a "logical newline", as described in perlrebackslash:

\n matches a logical newline. Perl converts between \n and your OS's native newline character when reading from or writing to text files.

And because it is so hard to tell I wouldn't want to change the meaning of $ without explicit request to do so for a single regex or within a lexical scope, i.e. by a flag or pragma.