There is at least one instance where --setParameter is not working as expected.

./build/install/bin/mongod --setParameter journalCommitInterval=200

Results in the journal flusher running every 100ms (default). By contrast

./build/install/bin/mongod --journalCommitInterval=200 

or using a config file works as expected.

Apparently the setParameter value is overwritten by the default value of the parameter in
https://github.com/10gen/mongo/blob/1eb33d31a32bb7d1a1a18e07c78239b90a9dd5d3/src/mongo/db/mongod_options.cpp#L433