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It should do, but best to check the Shimano Di2 compatibility document to be certain:
https://bike.shimano.com/en-EU/e-tube/project/compatibility.html
In terms of installation, it might work out the box, but you may need to ensure the firmware for each component is up to date.
Will an SW-S705 Alfine Di2 flat bar shifter control an Ultegra R8050 Di2 Rear Derailleur? And would it just be a case of unplugging the road shifter and plugging in the flat bar one, subject to cable length?