core subversion repositories (whether they come from soon to be removed "SVN Core" or migrated to svn plugin) are evaluated after the definition of php routes (that ends with .php)
Hence, nginx will be misslead that PUT /svnroot/with-svn-core/!svn/txr/9-i/foo.php is not actually intended to be a Tuleap php file but something that should be transfered to apache/svn