To keep track of how many operations have been applied in any phase,
it was possible to take a look at server logs:

log() << "replSet initialSyncOplogApplication applied " << n << "
operations, synced to " - << ts.toStringPretty() << rsLog;

Apparently this code has been removed
https://github.com/mongodb/mongo/commit/dbf18450b53d4ee1df99c701120567219608adc0#diff-04e89e83a90f31c93b1c3563db63c9c4L343