Unable to in-place update plugin in Dynamics 365 (with build or revision number changed)

UPDATE 19/9/18: It has been fixed in 9.0.2.5 version of Plugin Registration Tool https://www.nuget.org/packages/Microsoft.CrmSdk.XrmTooling.PluginRegistrationTool/9.0.2.5

If you use 9.0 version of Plugin Registration Tool to update your assemblies in Dynamics 365 you may encounter the following exception:

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