At the time of writing (2016-12) this doesn't appear to be possible programatically or automatically.  Pairing with devices can be carried out programatically where your app initiates the search and connection to a remote device, but there doesn't appear to be an api for incoming pairing requests.  To make the Windows IoT device discoverable to other devices requires use of the Windows IoT web interface which will prompt you to accept an inbound connection if you pair from a remote device.

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