Fix #5181 - when using --bundle in the CLI, use Embedded native gems when they are present and version compatible

Pull request overview

[ ] Model API Changes / Additions
[ ] Any new or modified fields have been implemented in the EnergyPlus ForwardTranslator (and ReverseTranslator as appropriate)
[ ] Model API methods are tested (in src/model/test)
[ ] EnergyPlus ForwardTranslator Tests (in src/energyplus/Test)
[ ] If a new object or method, added a test in NREL/OpenStudio-resources: Add Link
[ ] If needed, added VersionTranslation rules for the objects (src/osversion/VersionTranslator.cpp)
[ ] Verified that C# bindings built fine on Windows, partial classes used as needed, etc.
[ ] All new and existing tests passes
[ ] If methods have been deprecated, update rest of code to use the new methods

Labels:

[ ] If change to an IDD file, add the label IDDChange
[ ] If breaking existing API, add the label APIChange
[ ] If deemed ready, add label Pull Request - Ready for CI so that CI builds your PR

This will not be exhaustively relevant to every PR.

[ ] Perform a Code Review on GitHub
[ ] Code Style, strip trailing whitespace, etc.
[ ] All related changes have been implemented: model changes, model tests, FT changes, FT tests, VersionTranslation, OS App
[ ] Labeling is ok
[ ] If defect, verify by running develop branch and reproducing defect, then running PR and reproducing fix
[ ] If feature, test running new feature, try creative ways to break it
[ ] CI status: all green or justified