I don't see much that we can do here: the APK signing tool is the official one by Google, we didn't make it, and the build server just runs that. If you use a third-party tool, we can't support that - any issues will need to be taken up with the respective developer. (As with addons, this is another reason why you should choose third-party tools carefully and make sure they are actively supported and maintained in case they cause any problems.)
For general advice on building and signing Android apps, you can refer to Google's official documentation, such as Sign your app. You can also export Android Studio projects from Construct and continue to do building and signing with Android Studio, which Google's official guides also cover.