Fix chisel3 <> for Bundles that contain compatibility Bundles (Take 2) (#2031)

PR #2023 fixed a composition issue for chisel3 biconnects delegating to
FIRRTL partial connect when compatibility mode Bundles are elements of
chisel3 Bundles. It missed an important case though that caused
previously working code to break.

The bug is fixed by doing the automatic flipping for compatibility mode
Bundles that have "Input" as a direction in addition to those that are
"Flipped".