According to the documentation of ini_set(), it is possible to change the auto_append_file option anywhere within a
script. It would be nice to dynamically set the auto_append_file
option from within a php script and have it executed when
the primary script has completed. Although it's possible
to change it using ini_set(), the scripting engine has already determined which prepend and append file to use even
before calling the primary script.

Line 1381 of PHP_SOURCE_DIR/main/main.c confirms this:

retval = (zend_execute_scripts(ZEND_REQUIRE TSRMLS_CC, NULL, 3, prepend_file_p, primary_file, append_file_p) == SUCCESS);

Here's some pseudo-code to possibly fix this:

retval = (zend_execute_scripts(ZEND_REQUIRE TSRMLS_CC, NULL, 2, prepend_file_p, primary_file) == SUCCESS);


if (PG(auto_append_file) && PG(auto_append_file)[0]) {
     append_file.filename = PG(auto_append_file);
     append_file.opened_path = NULL;
     append_file.free_filename = 0;
     append_file.type = ZEND_HANDLE_FILENAME;
     append_file_p = &append_file;
     retval = (zend_execute_scripts(ZEND_REQUIRE TSRMLS_CC, NULL, 1, append_file_p) == SUCCESS);
}