The 50 over final doesn't clash with the 100, so in theory the two sides in the 50 over final could select their 100 players. But that might involve difficult conversations with the players who have done the hard work in getting their county to the final, only to be left out. I'm sure some counties might stick with the players who got them there, should they be fortunate enough to be one of those two finalists.
Then again, I suppose it's not much different to City or Liverpool using their second XI in the league cup, only to suddenly play the big guns in the SF and final.