Anecdotal evidence I know, but I was just in Ste. Genevieve County on Friday and the number of Trump signs and flags I saw was disheartening. This county is ancestrally Democratic and still contains a core constituency of union households (mining mostly, the county voted against Prop A in 2018 with over 80 percent rejecting the right-to-work ballot initiative) but it's also heavily Catholic and full of German and French Americans. I highly doubt Biden wins this one, but it's certainly the most likely to flip among the rural counties in Southeast Missouri.
St. Charles and Greene are not happening. While voters did approve the expansion of Medicare initiative in August, they're just still too Republican. I agree that Clay and Platte will probably be the two most likely to flip to Biden, then possibly Ste. Genevieve and maybe Iron, St. Francois, and Washington in the Lead Belt region of the state if Biden has a really good night.
Populist Ste. Genevieve will have a lot of Trump-Galloway voters. I think the entire southeast is lost for Presidential races, though. Iron and Washington are West Virginia-style R nowadays. St. Francois stayed R even in 2008, so Biden has no chance at all there.
Biden flipping any rural counties at all would require winning the state.
If he does manage that somehow (who knows, maybe 2020's polling error is the size of 2016's in the opposite direction, or something), the counties to flip would be the non-southeastern ones from the Kander 2012 and Galloway 2018 maps.