I’m not aware of any such rule set by WordPress. If I create a file generic.html in my root WP folder and then go to www.mypage.com/generic.html the file will open.
What exactly happens when you put the file into your root folder (next to wp-config.php)?
In any case, if there are rules in .htaccess that are causing some form of redirect or denial you could just remove those for a few minutes while Google pokes at your page to check for the file. The check only needs to happen once after all.
An alternative is if you already have the page in your Google Analytics account you can choose “Alternate methods” on the Webmaster Tools screen that tells you to upload the .html file and that will just prove your ownership from your Google Analytics account.