No circuitry is being bypassed, but it does not need to be.So that means that the amp of the Chord Mojo 2 will be bypassed when i connect the headphone socket to my external amp?
You can happily run any amplifier from the output of any DAP/Dongle/Device regardless of whether it was/was not designed to drive headphones or not. The reason being that amplifiers have incredibly high input impedances and so they pull almost no current from the source device.
'Double amping' is usually a concern not for any inherent reason that feeding an amp with another amp is bad (other than that you usually would want to avoid extra stuff in the signal path if possible), but simply because the output of an amp can often go much higher than the standard 2v RCA or 4v XLR, and so it may clip the device you're feeding.
If you ensure you set your amp to output equivalent of line level (2v RCA / 4v XLR) then it'll work fine.
This includes the Mojo 2. Just set it to 2v as rob explained how above and you're good to go