Yes, this is by design. Historically SQL Anywhere has used four numbers: major, minor, patch, and build number. Since SAP has acquired Sybase and the SQL Anywhere product the external number for SQLA now only uses three numbers - major, minor, and build number - since this is the SAP standard. Internally SQLA continues to use the four numbers.

So what is your question?

FWIW here are a two topics from the InstallShield 2012 Help...

Specifying the Product Version

InstallShield 2012

When you are specifying the version number for your product, you must ensure that you enter a valid product version. The version must contain only numbers. It is typically in the format aaa.bbb.ccccc or aaa.bbb.ccccc.ddddd, where aaa represents the major version number, bbb represents the minor version number, ccccc represents the build number, and ddddd represents the revision number. The maximum value for the aaa and bbb portions is 255. The maximum value for ccccc and ddddd is 65,535.

At run time, the installation registers the version number of the product that is being installed. The entire version string is displayed in Add or Remove Programs. The product version number is important because the installation engine uses it in part to determine whether to apply an upgrade.

You can configure the product version in the General Information view.

Note that although you can include the fourth field (ddddd) when you specify your product’s version, the installation does not use this part of the product version to distinguish between different product versions.

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ProductVersion Property

The value of the ProductVersion property is the version of the product in string format. This property is REQUIRED.

The format of the string is as follows:

major.minor.build

The first field is the major version and has a maximum value of 255. The second field is the minor version and has a maximum value of 255. The third field is called the build version or the update version and has a maximum value of 65,535.

Remarks At least one of the three fields of ProductVersion must change for an upgrade using the Upgrade table. Any update that changes only the package code, but leaves ProductVersion and ProductCode unchanged is called a small update. The three versions fields are provided primarily for convenience. For example, if you want to change ProductVersion, but don't want to change either the major or minor versions, you can change the build version.

Note that Windows Installer uses only the first three fields of the product version. If you include a fourth field in your product version, the installer ignores the fourth field.

Requirements Version Windows Installer 5.0 on Windows Server 2008 R2 or Windows 7. Windows Installer 4.0 or Windows Installer 4.5 on Windows Server 2008 or Windows Vista. Windows Installer on Windows Server 2003, Windows XP, and Windows 2000. See the Windows Installer Run-Time Requirements for information about the minimum Windows service pack that is required by a Windows Installer version.

Besides the obvious inconsistence between the external and internal numbers in v16: As long as the external version number format stays consistent for a particular major version, I guess there should not be problems with MSI files in that respect.

It would be different if it would also change for older versions, too, say, from 12.0.1.3942 to 12.1.xxxx, apparently.