The standardize name is 'Saint Louis,Saint Louis (City),Missouri' and the the CountyChecker offers 'Saint Louis,St. Louis,Missouri' or 'Saint Louis,St. Louis City,Missouri' I wish they'd both use the same standard!
Unfortunately, I think the variance is because there seems to be separate data sources for the features you are trying to use, likely because that is how they are available to the programmer.
When County Check is enabled, and a place name gets entered into the Place field for a Fact, a check is made for :quote: ~valid~ :unquote: county names within the state entered. Possible valid historical matches are displayed in their corrected form and an <Info> button can be clicked for the historical usage context of each offering. The user gets to either select from the :quote: ~valid~ :unquote: County Check place names -or- decline any change to what you've entered.
As for the Standardized place names offered, I believe they come from the Gazeteer. Keep in mind this is merely a 'suggestion'. Once GeoCode recognizes the entered place name and has filled in the Latitude/Longitude and Standardized place name, you can change the Standardized place name to whatever you want (it's obviously not used for County Checknor reports).
--- "GENEALOGY, n. An account of one's descent from an ancestor who did not particularly care to trace his own." - Ambrose Bierce
--- "The trouble ain't what people don't know, it's what they know that ain't so." - Josh Billings
K e V i N