We are running mongod on an embedded device (sounds weird, I know...), and since we have no RTC on the device, it always starts from epoch.

This makes the logging at startup likely to fail after a few boots, since the _id key is constructed from the system hostname appended with the milliseconds since epoch:
https://github.com/mongodb/mongo/blob/master/src/mongo/db/db.cpp#L215

Would it be possible to make the index key an auto incremented value or something similar?

Until now, I have mitigated the problem by removing the startup logging entirely from db/db.cpp:
https://github.com/mongodb/mongo/blob/master/src/mongo/db/db.cpp#L647

Can this cause be problems in other conexts?