My hack only alters URLs in templates, not URLs that were generated in the php files themselves. If you want to fix problem #1 you illustrated, you would have to start editing PHP files. It's a trade off whether you want to be 100% SEO'ed or whether you want the hack to be self-contained. For me, I don't care about it redirecting to the non-SEO'd version as long as the spiders get a taste of newpostinthread.html and lastpostinthread.html

To answer your second question, I didn't bother SEO'ing this because spiders never see the online.php page, it should be set to members-only access.