The fix in
TOOLS-2379 for old indexes relies on applyOps, which isn't allowed by the MongoDB Atlas shared tier proxy. To address this, mongorestore should ensure that only valid, supported index options are sent. A white list of options may be found in index_descriptor.h (though not all appear to be documented options).
Open question: should this behavior require a flag? Or should it be a fallback only if the initial creation errors? The goal either way should be to allow someone to use a modern mongorestore to restore a legacy dump to a legacy server.