What?
Is this a complaint about filename order or UTF-8??? Filenames have nothing to do with the titlebar anyway, the titlebar shows the title metadata and format of the book.
(PDF, lousy format that it is, has flaws in its support. Filename is used instead.)
As for filenames containing underscores, that occurs when invalid characters exist in the metadata. For instance
The period should never appear multiple times in a row, or at the end of a filename. Perhaps there is a bug whereby this transformation is applied on each field rather than the whole filename -- because that period seems safe to me.
P.S. calibre understands UTF-8, I have no idea what you are trying to suggest. Nor have you actually said what you think is wrong with calibre's support of UTF-8.