The storage engine of the node will determine its own compression. So the instance you are reinitializing should have the compressors configured.
Stop the node to update. Remove the data files. Add your desired compressor configuration. Start the node.
With a set of sampledata you can observe the difference with the third node with the blockcompressor enabled.
All of these are brand new replicaset members before chaning the 3rd node.
$ for l in a b c ; do mongo --quiet --host mongo-0-${l} --eval "db.getMongo().setSecondaryOk(); db.adminCommand('listDatabases').totalSize" ; done
159854592
159002624
107610112
The manual says it starts the oplog copy when the initial sync starts. So I don’t think that will be an issue.
But this is a lot of data to scan from compressed blocks and transmit. I don’t have any tricks to speed this up.