Hi Jason, it’s been a long time!
Index building changed in 4.4 with the release of the “simultaneous index builds” feature. This enables building indexes on the primary and secondaries simultaneously. An index build is committed when a majority of nodes have successfully built the index. The specific ticket that removed support is here: SERVER-41554. As that ticket mentions:
Applications previously running applyOps with an embedded createIndexes command will need to be converted to invoke the createIndexes command directly.
Hope this helps at least explain the reasoning behind the change.
Dan