flags is currently used for power of 2 allocation and is probably not applicable to the other storage engines. The server should error out to warn the user instead of silently ignoring it.
Sample shell session connected to a mongod running on wiredtiger engine:
> db.runCommand({ create: 'usd', flags: 0 }) { "ok" : 1 } > db.runCommand({ listCollections: 1 }) { "collections" : [ { "name" : "usd", "options" : { "flags" : 0 } } ], "ok" : 1 }