There's some info on Ross-Tech about how to do it with VCDS if you have a BRAND NEW transponder to add. Needs a PIN for the system though....
Don't think it works with any used/secondhand one.
Seat memory knows (if you enable it) which key unlocks the car. A clone will be a clone so not separate........
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2003 D2 FL S8. Irish Green Pearl/Beige. Solar sunroof, auto-dim mirrors, electric rear seat functions and extended leather. Ski hatch retrofit. Aftermarket reversing camera. DVB-T and XCarlink now removed as redundant.
2016 Volvo V40 T5 Cross Country (4WD) with ALL the toys including adaptive cruise etc. etc. Osmium Grey with Blonde/Charcoal leather interior. Polestar performance "optimisation".  (Even rarer than a D2 S8!) Oh, and a brand new engine at just under 30,000 miles on the factory one! 
Finally: gone, but not forgotten.....
1998 D2 PF S8. Agate Grey/Platinum. Every option (I think) except electric rear seats, Tiptronic steering wheel, ski hatch, towbar & dimming door mirrors.
e.g. Cruise control, NavPlus/TV, Bose, GSM, Xenons, Solar roof, Parking sensors, Alcantara/leather everywhere of course.  (internal dimming mirror added later)
1998 (very early) Ford Focus 1.8 Zetec; ABS/TCS, Heated screen/mirrors, Aircon. Added Auto-dim mirror, Leather seats, Trip computer, Cruise control, OEM Ford SatNav with CD changer.
And before that a lot of Rover 800s, a few oddities, a lovely Triumph Dolomite 1850HL with Overdrive and way back in my schooldays an Austin Seven aka Mini 850!
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