You should have a .qsf, so can you just put it in there? You always need a .qsf since the number of things in it quickly dwarf the ability to put everything into the actual command line options, such as pin locations and IO standards.
I run the following everyday for multiple project:
quartus_sh --flow compile --64bit <project_name> -c <revision_name>
(The <project_name> is just the name of your .qpf without the extension, and revision_name is the name of your .qsf with the extension. The -c <revision_name> is only necessary if it's different than the project_name.)
If you really need to change a lot of options at the beginning of the compile, I would recommend scripting it, either with a pre-flow script or something else, but for the most part I don't believe they're overly necessary.
