the following is a trivial patch for those needing a workaround to this problem.  it only inhibits the munging of dots and doesn't address things like spaces and square brackets.  it also doesn't address introducing an INI setting.

diff -ru php-5.2.6._dist/main/php_variables.c php-5.2.6._mine/main/php_variables.c
--- php-5.2.6._dist/main/php_variables.c        2007-12-31 07:20:15.000000000 +0000
+++ php-5.2.6._mine/main/php_variables.c        2008-06-14 23:34:25.000000000 +0000
@@ -91,7 +91,7 @@
 
        /* ensure that we don't have spaces or dots in the variable name (not binary safe) */
        for (p = var; *p; p++) {
-               if (*p == ' ' || *p == '.') {
+               if (*p == ' ' /*|| *p == '.'*/) {
                        *p='_';
                } else if (*p == '[') {
                        is_array = 1;

In PHP 5.4 INI the register_globals setting was removed finally. So, this atricle in documentation become not true:

"Dots in incoming variable names

Typically, PHP does not alter the names of variables when they are passed into a script. However, it should be noted that the dot (period, full stop) is not a valid character in a PHP variable name."

Because external variables will never become internal variables, translation dots to underscores become senseless. 

Please, add an INI setting to disable dots to underscores translation!

Has there been any progress on this?

As I understand, requirement of convert dots and spaces to underscores inside $_GET variable and in result of parse_str() was "Using Register Globals" ("because variables in PHP can't have dots and spaces in their names").

Now "Using Register Globals" was removed in php 5.4.0!
But convert dots and spaces still here...

Can you add option in ini-file and argument for parse_str() to do not convert dots and spaces?

INI options sound easy but they can make writing portable code difficult and so are avoided whenever possible.

This subject has come up recently on the internals mailing list as something to reconsider for PHP 8.
https://php.markmail.org/thread/e2wpxygeblezyzf2