I don't think you can, not with ebook-convert or ebook-meta.
ebook-meta is for setting
user-facing metadata, like title, series, author, publisher, etc.
You cannot set
formatting metadata with it.
As for ebook-convert, it relies on calibre's Input/Output plugins, which do not understand Fixed-Format.
The fact that they sort-of-resemble Fixed-Format books is incidental.
It should be easy to unzip the epub though and insert the right meta tags with awk or sed.
You can also use a vimscript, since if your EDITOR=vim then
Code:
calibre-debug --explode-book $joinedfilename.epub
will open directly with vim.
Now, even if you do that, I'd still want to check the book to make sure it works as expected.