This was on my list too about some little things I found in the spreadsheet.
It´s not only the manual, the game is rated as "eC" or "Early Childhood" (I think it´s the only with "Richard Scarry´s Busy Town" to have this badge in the front artwork). Both have the same number 670-4070 but in the variant the code was moved below the UPC to make room for the early childhood rating/explanation.
The other difference is the variant has white letters for the GENESIS as well as the mark "Registered" instead the "Trademark". Also the 1996 date and SEGA address.
The cartridge label seems to be the same. The back shows "Assembled in the USA".
Hopefully this helps. I will check my notes and let you know about the other couple things in the spreadsheet.