Further work on this topic also showed that the error was also being caused when the detection rules for the App are not configured correctly. In the IntuneMDMDaemon logs on the endpoint Mac, you'll see:
AppInstallManager+Logging | Error processing app. PolicyID: xxxxxxxxx-xxxxxx-xxxx-xxxx-xxxxxxxxxx, AppName: yourappname, AppType: PKG, Error: AppDetectionError.errorGettingBundlePathFromBundleID
Extract the contents of your PKG with pkgutil, check the contents of the info.plist for the CFBundleIdentifier and CFBundleShortVersionString values, and adjust your detection rules accordingly.
Don't trust Intune to identify correct detection rules for custom pkg files. This has sorted all my issues surrounding this error