All the top 4 mons can be screwed over by Klefki in a way or another:It's a liability against the entirety of the top 4. That fact alone should keep it out of S- unless we're considering parahax as a efficient means of checking which admittedly is true if you're a luck God but that generally isn't reliable.
Pdon = free switchin
Ekiller = para is almost beneficial since it can't get burned anymore
Xerneas = admittedly this is probably klefkis best matchup assuming non block geoxern AND even if it isn't then klefki still faints bar massive para hax. If it's non scarf/blockless geoxern then klefki is outright set up. though keys spikes on cm so I guess that somewhat cancels out.
Mence = carries refresh and/or EQ more often than not and it's really not that difficult for mence to find turns to refresh, and keys cannot safely switchin due to fear of Eq.
Moving alongside S rank, klefki is still food for ho oh and kyogre which is also a turn off since keys having so many common and prevalent threats stopping it isn't really good for S- rank. A+? Sure since it does provide utility but it's utility just simply isn't great enough for it to be S-
Edit: better than latis? Arguable but they do completely different roles and Latis are still technically more splashable. No way in hell is klefki more viable than ho oh though
P.Don: hates Toxic, not a safe switch in. Also vulnerable to Spikes.
Arceus: non Refresh/Lum Berry variants hate Toxic, other variants are forced to set up an extra turn if Klefki has Reflect. Hurt badly by Foul Play.
Xerneas: Klefki is the best Xerneas check in the game, I shouldn't even need to explain this. Block GeoXerneas is a gimmick in a tier where Mega Gengar exists and shouldn't even count.
Mence: hates Fairy STAB and suffers from the same issues as Arceus.
Ho-oh hates Thunder Wave/Toxic as well as Foul Play and Lati@s just flat out lose, so RestTalk P.Ogre is the only reliable counter to Klefki (purely offensive variants force Klefki out but will be crippled if they switch into status). A support pokemon that gives issues to almost the entirety of the S-ranked pokemon should be S-rank as well.