Inserts into any namespace ending in ".system.indexes" are treated like inserts into "system.indexes" and actually build indexes.

> db.dropDatabase()

{ "dropped": "test", "ok": 1 }

test[13:4:8]> db.foo.insert({a:1})

Inserted 1 record(s) in 1057ms

test[13:4:14]> db.system.indexes.find()

{ "v": 1, "key": { "_id": 1 }, "ns": "test.foo", "name": "_id_" }

Fetched 1 record(s) in 1ms

test[13:4:21]> db.foo.find({a:1}).explain()

{

        "cursor": "BasicCursor",

        "isMultiKey": false,

        "n": 1,

        "nscannedObjects": 1,

        "nscanned": 1,

        "nscannedObjectsAllPlans": 1,

        "nscannedAllPlans": 1,

        "scanAndOrder": false,

        "indexOnly": false,

        "nYields": 0,

        "nChunkSkips": 0,

        "millis": 0,

        "indexBounds": {

        },

        "server": "ubuntu:54321"

}

test[13:4:27]> db.randomNS.system.indexes.insert({ns:"test.foo", key:{a:1}, name:"a_1"});

Inserted 1 record(s) in 1ms

test[13:4:41]> db.system.indexes.find()

{ "v": 1, "key": { "_id": 1 }, "ns": "test.foo", "name": "_id_" }

Fetched 1 record(s) in 1ms

test[13:4:55]> db.randomNS.system.indexes.find()

{ "v": 1, "key": { "a": 1 }, "ns": "test.foo", "name": "a_1" }

Fetched 1 record(s) in 1ms

test[13:5:3]> db.system.namespaces.find()

{ "name": "test.system.indexes" }

{ "name": "test.foo.$_id_" }

{ "name": "test.foo" }

{ "name": "test.randonNS.system.indexes" }

{ "name": "test.foo.$a_1" }

Fetched 5 record(s) in 1ms

test[13:5:10]> db.foo.find({a:1}).explain()

{

        "cursor": "BtreeCursor a_1",

        "isMultiKey": false,

        "n": 1,

        "nscannedObjects": 1,

        "nscanned": 1,

        "nscannedObjectsAllPlans": 1,

        "nscannedAllPlans": 1,

        "scanAndOrder": false,

        "indexOnly": false,

        "nYields": 0,

        "nChunkSkips": 0,

        "millis": 0,

        "indexBounds": {

                "a": [

                        [

                                1,

                                1

                        ]

                ]

        },

        "server": "ubuntu:54321"

}