If the regex were really anchored (that is, immovable), it would find the end of the string, and then match the regex in that context -- that is, the regex would have to terminate at the end of the string. As it stands, Perl can't optimize the regex that way, and we end up matching EVERY chunk of whitespace, and then testing to see if END-OF-STRING comes after it.
IMO, you shouldn't care about the internals of the regex engine, but about the meaning of the regex you are writing. The exact algorithm and optimizations that the engine uses may change from one version to the next, but the meaning of /#(.*?)$/ will always be the same (at least for Perl 5 ;-)