A Spy fighting a villain he previously spoke with would get the +1 to Guns (among other bonuses) from Scoped Out. Then if he switched from Guns to Martial Arts, he'd get +1 to Martial Arts from Scoped Out and +1 from Integrated Training for a total of +2.
Personally I would rule that a Martial Artist taking Signature Weapon on her nunchaku wouldn't change the Damage from Whirl of Fury, because it specifies a set Damage Value rather than a modifier. The signature nunchaku would be 11 damage (8 base +3 from Signature Weapon) under normal circumstances, but I'd say Whirl of Fury would still make it 14 damage.
And in the case of the Supernatural Creature, the "Conditional Escalation" signature schtick and "Goldenheart Monster" creature schtick have literally the same effect, so it's my belief that they're the same schtick and it's a mistake that they're listed with two separate names. Until we get an errata with more details, I'd say a Supernatural Creature already has "Goldenheart Monster" and couldn't take it again.