Well, it kinda depends how you look at it. It's reasonable to take the fact that Abilities are specified as being directly reducible, but other stats aren't, to mean that you can only lower Abilities. However, Reduced Trait definitely applies to any sort of trait, and uses the rule that the PP gain is equal to the value of the traits reduced.

Since pretty much anything can be an Enhanced Trait, if you don't want your Stamina to be subject to Nullification, you can pick some other essentially constantly active power you have, make some or all of it an Enhanced Trait rather than a base trait, and apply the Reduced Trait to that. If it gets Nullified the penalty goes away, but since you're already at your PL limits, the stat doesn't increase.

But since that option is always available and carries no point difference, I tend to just figure that the reducing abilities section is meant to be illustrative, or perhaps to clarify the rules for reducing Abilities below 0 (which is what's actually being addressed there), and work off the assumption that they didn't specify rules for lowering other traits because those rules can be derived from basic math; if adding four ranks costs 4 PP, then lowering the rank by 4 returns 4 PP.

There is also precedent for adding extras directly to traits bestowed from Abilities (for example, you can add extras to or even build alternate effects off of your basic Strength Damage, and you can add Impervious to your Toughness gained from Stamina). Which suggests that it would be equally valid to do, say, raw Stamina 14 (4 ranks Limited [Only for Toughness]). Or maybe attach Quirk 4 (-4 Fortitude) to your Toughness from Stamina or, really, whatever power you want to attach it to.

Now, if your GM is steadfastly against lowering bonuses from Abilities for some reason, then yeah best you can do is take like Stamina 10, and then buy Protection 4, and accept that Nullifies will eat four points of your Toughness. Or pay the 1 PP surcharge for Innate. Neither's the end of the world. ...Although if you have at least five other points of permanent powers (let's say Regeneration 5, for example), you could do something like Dodge/Parry 10, Stamina 10, Will 10, Enhanced Trait 9 (Regeneration 5, Protection 4; Permanent, Reduced Dodge 4, Reduced Parry 4). That comes to 51 points. Dodge/Parry 6, Stamina 14, Fortitude (-4) 10, Will 10, Regeneration 5 would also come to 51 points. Comes out the same, and if your powers get Nullified your stats snap back to straight 10s rather than having a four point deficit.

...What I'm saying is there's lots of ways to reduce traits to avoid wasting points on stuff you don't want, so to me it just makes sense to figure you can do it in the most straightforward, mathematically-obvious way, even if that isn't spelled out explicitly.

(Also long-lasting Simultaneous Nullifies are overpowered anyway so anything that makes them less effective is only going to improve game balance, not worsen it).