LOL! The funny thing is I've got the exact opposite
I've got a few Omnibus editions and I would prefer to have the individual titles within calibre's database rather than the Omnibus Title. Right now I am entering the Omnibus Title, Series Name and Series Index # (as appropriate to the whole series). This prevents issues within large series where books 1-10 are individual and then 11-14 are an omnibus edition, listed as 11. I enter the names of all book titles within the Description / Comment field. This does alter the book numbering though (what should be book #15 is now listed as #12 which is the right order, but the wrong number - strictly speaking). For real world examples, think H. P. Lovercraft (and any of the numerous adherents who increase the Cthulhu Mythos every day), or Agatha Christie, who both have had books published in multiple formats, multiple titles, multiple omnibus editions, etc. To know what is in the book
is more important than the book title.
But personally I am finding that this does not work all that great. I have several Omnibus, let alone Anthologies. And then their are Manga and Magazines... Those two get very, very ugly to deal with.
I've wondered if adding a new field, Book Title (and renaming Title to Story Title), would allow Books and Stories to be differentiated without adding too much extra work or overhead. Of course, calibre would also need to support something like the HTML anchor function so you could click a story and jump directly to that story instead of the first page of the book.
A somewhat related issue is version numbers for books. If we're all making corrections to typographical errors, adding TOCs, altering format for readability, etc there should be a means of keeping track of the books version number. Otherwise you cannot know for certain which version is the most up to date.