Hmmm, it would seem to me that the -3 is applied. The only place I see that calls out FtF is in the MA rules and this is decidedly not that. Also, there is precedence for it not needing to be a FtF in skills like Mimetism (which would apply the -3 even if you just idled).
Check the example for dodging vs. a mine and shooting. Modifiers caused by the mine don't bleed through to the dodge against the BS Attack. Mimetism doesn't need to be a Face-to-Face roll to apply because it's described explicitly as a modifier that applies when those skills are targeted at the trooper. Likewise, Surprise Attack's MOD would apply even in a normal roll situation because it says "applies to any Skill Roll that those targets perform in ARO."
That's a really awkward way to determine that. Look at CC Attack (-3). From reading just the rules (and not interpreting the example), as best as I can tell that works by applying a -3 MOD to the target of the CC Attack irrespective of whether the target's Skill Roll is in opposition to the CC Attacking model. There needs to be an "for Rolls against the user" (or similar text) in the negative MOD rule itself. IE: "A negative MOD (-) in round brackets next to a Special Skill, Weapon, or Equipment will be applied only to enemies acting against the user." Instead of: "A negative MOD (-) in round brackets next to a Special Skill, Weapon, or Equipment will be applied only to enemies." Edit: The phrase "or to those enemy Troopers acting against them" appears later on Page 60 (in the grey box as part of the introduction of the examples) but it'd be clearer being in the main rule. Also, it runs into the fact that it suggests negative MODs can only be applied to enemy Troopers.
The example in the grey box is a skill that explicitly says when the modifier applies. Consider the situation: 1. Active player does Move into base contact 2. One reactive model declares Reset. Another declares BS Attack along the path. 3. Active model declares attack with Para CC weapon. What’s the -3 MOD apply to? Especially considering that if that was a modifier on a CC skill, it would be subject to: Opponent MOD: A MOD applied to the Attribute of an enemy when making a Face to Face Roll.
I'm not arguing how it works, I'm saying that in the governing rule itself it should make it clear how it works.