
The mischief caused by 404.php template is not a problem for authentication, when I stumbled into Yahoo!'s Site Explorer. To claim your site, you were instructed to place a special file with special content under / of the site. This way, one GET will do and have no problem with customized 404 pages. The latter is pretty common in use for sites managed by a CMS (Content Management System) or blogging servers. I wonder how come the smart engineers at Google decide to do two GET instead...
Once I added the required file on my wordpress.org blog server's / and clicked to continue, the next page asked me to keep the file there for 24 hours, till Yahoo's bots take their sweet time to crawl, literally! To a sharp contrast, Google's webmaster tool authenticates site ownership real-time, and sucks in sitemaps real-time too!
Placing a special file under / is the only way to authenticate your ownership on Yahoo Site Explorer. For millions of hosted sites (blogs or otherwise) whereas content owners don't have access to the /, they'd be out of luck. For now, at least. Hopefully when Yahoo! Site Explorer comes out of beta, they'd come up with a way to authenticate sites whose content owner have content-level access (META tokens, maybe?) instead of file-level access.
In comparison with Google's web master tools, Yahoo's site explorer is so spartan right now. Its own blog hasn't been updated for a few months now. I guess it is real beta then.