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Here's one way to look at it: if it's not an Action, how can it be a Matrix Action?
I assume this references threading and fully agree. It can't have it both ways by being "part of the program's action" but count as a separate action for it's own bonus. It's not even a Free Action, it's a "No Action - as part of another action". As TE said though, to each their own.
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Now this does beg the question, does sustaining give a -2 defenses?
I didn't find anything specific one way or another, so going into "this is how we play at my table" land, here is how I rationalize it.
First we must make sure we clearly distinguish the Defense test vs the Matrix Damage Resistance test. Though it never really addresses the wound modifiers for Matrix damage (other than in the IC combat example), IMHO they do apply to the Defense test, as a parallel to how physical combat works in regards to Defense and Damage Resistance. (I know you're asking about sustaining modifers, but I figured this would be a good example to start with and show what the basis of my interpertation is).
I think all modifiers apply as normal to Defense tests, that includes the +2 for hot sim, sustaining penalties, and (matrix) wound modifiers. Damage Resistance gets none of these however, as it's the consequence of the Defense tests (not even a counter action), so it's not limited by or gaining any benefit from modifiers. To me, it's a raw (and RAW) mechanic that is straight forward representation of how bad that hurt. Thus moving faster or already being hurt don't/shouldn't really factor (as that was already covered in the Defense test that predicated the need for damage resistance).
In short, Defense tests are penalized by sustaining modifiers (unless you're sustaining only the shield complex form, as sustaining modifiers explicitly do not apply to the test that they modify directly). Finally, the sustaining modifier applies to all TM actions, including purely physical ones (when sustaining threading in AR for example but taking a physical pass or action).
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Also, what about fading? Do you get the +2 to resist fading while in the Matrix?
To me Damage Resistance, Drain, and Fading all amount to the same thing. Given the above, no modifier nor penalty is applicable. They are straight forward "you got damaged, let's see how bad". In the case of Drain or Fading, you're just damaging yourself directly, without anyone helping you out. (I bleed for you guys!)
So I'd say no, Fading gets no hotsim modifier (nor wound or sustaining penalites). Drain works the same way for us.
That being said, I can feel myself stretching, and can very well be proven wrong, but based on my experience with SR4, and my more recent experiences with SR4A, I don't see anything concrete one way or the other. This is what works for us as it serves the dual purpose of being both intuitive and ensuring that resisting damage of any kind doesn't become a reciprocal nightmare of devolving dice pools. (Minor Edit: Or that one doesn't accumulate so many modifiers as to make resisting damage irrelevant and leading to game breaking dice pools since the risk limitation is effectively removed)