What Makes an macOS "Package" Show as a Package?
Short answer

To register a document as a package, the developer of DayOne would have had to modify the document type information in the DayOne app's information property list (Info.plist) file.

Long Answer

A package is a file system directory used by macOS and iOS. It's basically a directory that will appear as a single file, but which may in fact contain a preserved state of files and folders. So, a folder could have a number of subfolders and many files, but as a package it will be displayed to users like a single file. For example, in macOS the Finder will see a package as a single file to avoid users mucking around with the actual  contents. However, users can view the contents through various methods such as right-clicking on the package and selecting Show Package Contents from the context menu.

Apple's Bundle Programming Guide, available on their Developer site, has a whole section on Document Packages. Below are some relevant quotes:


  To register a document as a package, you must modify the document type
  information in your application’s information property list
  (Info.plist) file. The CFBundleDocumentTypes key stores information
  about the document types your application supports. For each document
  package type, include the LSTypeIsPackage key with an appropriate
  value. The presence of this key tells the Finder and Launch Services
  to treat directories with the given file extension as a package. For
  more information about Info.plist keys, see Information Property List
  Key Reference.
  
  Document packages should always have an extension to identify
  them—even though that extension may be hidden by the user. The
  extension allows the Finder to identify your document directory and
  treat it as a package. You should never associate a document package
  with a MIME type or 4-byte OS type.


Source: Bundle Programming Guide

On the off-chance you can't access the document, let me know and I'll include some additional quotes from the page.