Why don't you save the data as a CSS file, and then parse, load, and save back to that file when the user wants to make changes? Then you don't need to worry about generating the file when it's requested.
You can use the serialize function to put the data into a format that can be stored in a MySQL database field. On retrieval you would then use the unserialize function to restore the variable.
The best solution would probably be to use a dynamic CSS file. Save the values as an array in your database and pass them to a PHP file masquerading as a CSS file to set the dynamic values. Check this out: Embedding PHP In CSS
I think Mongodb would be perfect. You could keep your default CSS and then only overwrite the fields that the user has entered. I also think a relational db like mysql would just get in your way.