Through the years I've had many opportunities to "reverse engineer" proprietary files, and I noticed that many times these are "disguised" ZIP files which just pack standard XML, HTML, config and raw text files. However, I don't understand why would the developpers do that.
A few examples on top of my head of these "disguised" file formats are:
There are many other files formats of this sort, and sometimes even company that really don't want their data files to be publicly read rely on this disguised ZIP to store data (like games saves).
What are the technological advantages of ZIP files over custom file types ?
Is there a name for the practice of building a (sometimes proprietary) new file format on top of ZIP ?
If you want your new file format to be interoperable by other applications, you'll need to define your format completely. Building on top of other standards, such as ZIP, XML, and HTML cut down a large part of documents and maintenance effort.
The format designer is usually also the first implementor. Using existing standards means they can use existing, known to be correct and working tools to create and read. This means Microsoft Office file format designer, for example, doesn't need to debug serializing and deserializing logic since they're already using the industry-proven XML.
Using a compressed archive instead of plain archiving such as TAR means your format automatically reduces the required storage when possible. ZIP is an ISO standard and patent-free (as long as it's not encrypted with a strong algorithm), so the designer and implementor don't need to pay for a license, unlike, say, RAR.
Implementing the consuming application on different hardware or platform may require rewriting a large part of code unless it's built on top of already popular standards. An EPUB reader, for example, can be patched together with the ZIP reader library (which is usually built-in with various frameworks) and HTML viewer. That's a near-zero effort from the developer side who can then focus on other features. Since the framework and CPU are likely optimized to handle ZIP compression, they usually perform much better than custom compression format. Another rarely considered factor is security and reliability. A custom archiving format may seemingly work faster or compress more efficiently, but on real-world data it might crash, or worse, return wrong reads which can result in a security breach or incorrect result.
As for companies not wanting their file to be read, plenty of solutions that can be built on top of ZIP. AES encryption is available as an open standard for ZIP under AE-x. Maybe they don't need to hide the entire structure, just values, they can encrypt the individual entries on the XML/JSON or files. EPUB DRMs can be broken easily, but that's going to happen regardless if the ebook was using non-zip based format.
I don't think there's a specific name for building a new format based on top of ZIP. When you want to store a string, you pick one of the available text encoding standards, if you want to keep the value secret, you encrypt it with yet another encryption standard, not invent a new encoding scheme. What those designers doing is simply taking the existing standards, and they're not just using ZIP, they're also using XML, Unicode, various image formats, etc.
About Microsoft formats being ZIP, well, not all of them. Pre-2007 Office files aren't, which is partly the reason behind the difficulties of implementing and improving the format (another reason is Microsoft deliberately prevent people from doing it in the first place by not documenting them). XLSB is ZIP, but instead of XMLs it uses binary serialization, which speeds up saving & opening, but afterward, it operates as fast and as memory efficient as XLSX file. ACCDB, like the precursor MDB, aren't ZIP files, database, in general, are allergic to being compressed. Visio transitioned slower, Visio 2010 uses XML based VDX (not compressed), then in 2013, it adds VSDX (XML and ZIP based), while Project and Publisher don't seem to be moving on new format soon. XPS, Nuget, and Appx are zip, but csproj, vbproj etc aren't. MSI installers are archives but they're not ZIP files.
It's interesting you stopped at JAR & WAR, because continuing on, Android APK files are ZIP files (which in itself may contain the content of the JAR it referenced), so does the overarching AAB. On iOS, IPA files are ZIP too. The LibreOffice default format, ODT, ODS, and ODP are all ZIP & XML based, designed around the same time as Microsoft Office's new format.