This may be because the size "mechanic" is be spread out through many different elements of the NWN engine, and this is the odd corner case of a (sub-)subrace (?) being a different size to the base race.
Size modifiers are apparently determined by the creature appearance (
appearance.2da) and the
Small Stature feat doesn't, mechanically, do anything. It's just an indicator that the size modifiers will apply to halflings and gnomes, not because of the feat but because of their appearance. It's unclear whether caliban runts are supposed to be medium or small, but if they have the halfling or gnome appearance, they should be small. It's complicated because size modifiers are often invisible on the character sheet.
Relative
weapon size might be something else, but it seems caliban runts are mechanically treated as medium for the purposes of determining what counts as a light or two-handed weapon (which means eg. that halflings cannot finesse a rapier, since it's two-handed for them), and whether they can wield large weapons at all (caliban runts apparently can).
Caliban runts also seem to be mechanically treated as medium for the purposes of Evard's Black Tentacles.
But caliban runts seem to be mechanically treated as small for the purposes of monk fist damage progression, which isn't in line with their being treated as medium above.
Not sure whether caliban runts are treated as medium or small for the purposes of knockdown attempts either.
