No configuration is required on the Nautilus itself, since the Nautilus sends and receives MIDI data in all of its modes, including Sequencer mode.
A MIDI data connection is required between the Nautilus and the MacMini. This could be via USB, or using the DIN MIDI connectors on the Nautilus, via a DIN MIDI interface to the MacMini (via the Babyface, possibly? I'm not familiar with the breakout cables on the Babyface, though there are several configurations available from RME). If using DIN MIDI connectors, MIDI In on the Nautilus should be connected to the MIDI Out on the interface, and Midi Out on the Nautilus should be connected to the MIDI In on the interface. Note that the different Timbres in Nautilus' Sequencer mode use different MIDI channels by default.
If the Nautilus is connected directly to the MacMini, it should appear as two devices over USB. A MIDI device, and an Audio device. Use the appropriate MIDI and Audio menus in Logic Pro to connect to the Nautilus. If using the Babyface as the audio interface between Nautilus and MacMini, then connect the Nautilus L & R outs to the Babyface Audio Ins on the breakout cable, and configure Logic Pro appropriately.
There may also be useful discussions elsewhere e.g:
https://www.logicprohelp.com/forums/top ... gic-pro-x/
Since the Nautilus and Kronos share many features, especially MIDI, do include the Kronos when looking for information.
Also, a couple of useful videos. These relate to Combi mode, but much should also be applicable to the Sequencer mode:
https://www.youtube.com/watch?v=nKyBqt9hsD4
https://www.youtube.com/watch?v=SVGfYIVaWWM
.