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
All the top 4 mons can be screwed over by Klefki in a way or another:
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.