Bugfix converter clearing flips (backport #2788) (#2832)

* Bugfix converter clearing flips (#2788)

* Bugfix: Output on Vec of bundle with mixed field orientations
* Bugfix OpaqueTypes clearing flips

(cherry picked from commit f05bff1a

)

# Conflicts:
#	src/test/scala/chiselTests/Direction.scala

* Resolve backport conflicts

Co-authored-by: Adam Izraelevitz <adam.izraelevitz@sifive.com>
Co-authored-by: Jack Koenig <koenig@sifive.com>
Co-authored-by: mergify[bot] <37929162+mergify[bot]@users.noreply.github.com>