This is an oldie. There are 4 slots for keys, not 3. Car came with 3. If you buy a car and it is missing a key and buy a replacement, then you are supposed to delete the missing key when you add the replacement. Because if you don't the missing key might show up one day, and your car is gone. This is why the dealer wants you to bring all the keys. To see which one is missing, and delete it. Or you can just put the replacement key in slot 4 if you do not think the missing key will ever show up.
I took the past 2 years off from Boxster stuff, but I doubt if key replacement things have changed. I guess they can now clone the chip so it will start, but not the remote. Looks like you still need the 24 digit code on the paper tag and a PST2/PIWIS for the remote.