The DFDLGeneralFormat.dfdl.xsd file defines two formats: GeneralFormat and GeneralFormatPortable. The idea being that GeneralFormatPortable can be used for schemas that want to work in both Daffodil and IBM DFDL.
However, GeneralFormat defines the extension property emptyElementParsePolicy that IBM DFDL does not allow. Even if a schema only uses GeneralFormatPortable, IBM still sees this invalid property in GeneralFormat and creates an SDE. This means anything using tthe DFDLGeneralFormat.dfdl.xsd file cannot be portable.
For his to work, the GeneralFormat and GeneralFormatPortable types need to be defined in completely separate files.