Programming Needed:
Strattec # 692246 5913978
ILCO # HD106-PT HD106 HD1O6

And all that means..........????

 Hey !Did you buy and use one of the correct required OE key blanks that Smog Tech listed to program a unique key ID to  , or did you just  buy  some unknown Chinese clone chip key off Amazon that K mart , Wallymart ,and  hardware stores and even some Lazy F@ck Locksmiths use to quickly make a Clone out of a working key ?

 Have the dealer parts guy look up the OE key part number by the VIN and then make sure you try a genuine Strattec key equivalent of that number and not a Chinese Knock off , and then you' ll know if the Honda knockoff software  on your Chinese scanner genuinely works :-)
My old DS708 with minimal ECU coding  once worked to program a key on a 2006 Acura TL so I think The better faster  MS 906 should be capable to do the same on a 2002 Honda Civic unless the key is not correct or Autel possibly dumbed down the software and it hasn't removed the non working function from the menu yet? I would give Autel the benefit of the doubt and try another key cut from a genuine Strattec blank first.