It's not really different meeples. Tuscany came with every special worker in every player color. They all were thematic to the card they went with, ie type of worker. It made for a TON of meeples that rarely got used.
In Tuscany EE, presumably to save cost and space, they switched it to one gray generic worker meeple to mark which special worker is in play. Since you can't use all of the workers at once anyway, this made sense. You then get a similar generic spec. worker meeple in your color to use on the board.
I've now seen some videos/photos looking into this, they are totally different than my original Tuscany. But that's ok, I get what they are trying to do. I like it.