If your MSI setup is expected to run on Windows installations that still support 32-bit applications, InstallScript custom actions can still be used. As things currently stand, the only version of Windows that does not support 32-bit code at all is Windows 2016 Nano Server. However, since Nano Server also doesn't support MSI installations, this requirement is irrelevant.
WOW64 support is optional on Windows Server 2008 R2 and newer, so there could be situations that these custom actions will not be able to run. However, since the majority of setup.exe based installers, including Microsoft's installers, are 32-bit, disabling the WOW64 feature runs the risk of not being able to install a number of software packages.
This error can be ignored unless you absolutely need to ensure that your setup does not contain any 32-bit install time code. If this is a requirement, a 64-bit MSI DLL action should be used instead of InstallScript custom actions.
