If you have the option of getting a bonus to some saving throws, don't you want a reminder of that listed on the Special tab? This is as intended.
It seemed like a pug, as I saw special abilities being something build in to a character, not from items carried and used. I understood the logic behind this after working up another punch of mid-level characters... and that leads me to next subject;
Example of character whose second trait isn't showing in special abilities.
Male Tiefling Magus 3
SPECIAL ABILITIES
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Anatomist +1 to confirm critical hits. 1st trait
Combat Casting +4 to Concentration checks to cast while on the defensive. Feat
Concentrate (1/day) (Ex) 1/day, reroll a concentration check at +4. Magus ability
Damage Resistance, Cold (5) You have the specified Damage Resistance against Cold attacks. Tiefling ability
Damage Resistance, Electricity (5) You have the specified Damage Resistance against Electricity attacks. Tiefling ability
Damage Resistance, Fire (5) You have the specified Damage Resistance against Fire attacks. Tiefling ability
Darkness (1/day) (Sp) Darkness once per day. Tiefling ability
Darkvision (60 feet) You can see in the dark (black and white vision only). Tiefling ability
Spell Combat (-4/-2) (Ex) Use a weapon with one hand at -4 and defensively cast a spell at -2 with the other. Magus ability
Spellstrike (Su) Deliver touch spells as part of a melee attack. Magus ability
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Missing trait is Desperate Focus: +2 trait bonus on concentration checks.
I think there is fundamental flaw here (in my thinking). I am looking special abilities to be something easy for GM to track what Feats / Traits / Other Abilities the character has picked up. But instead Special Abilities is showing factors that have not been build in to a statblock (whether it is gear, trait, feat or other ability)?
Example: This character has also Dodge feat, but there is no point listing Dodge in Special Abilities because it has been already calculated in to AC.
AC 17, touch 13, flat-footed 14. . (+4 armor, +2 Dex,
+1 dodge)
That leaves me a question, why all 3 elemental resistances are in special abilities? As statblock shows:
Resist
cold 5, electricity 5, fire 5