Most of them, yes. The only sliders I've found to make a real difference are Holding, False Starts, Clipping and Facemasks, but those seem to actually to (set Facemask on 100 for one game, on 0 for another if you don't believe me. The Facemask animation is quite obvious, if the slider is at 100 every Facemask penalty committed will be called, with it lower, you still see the animation, but it doesn't get called every time). As you've observed, intentional grounding NEVER gets called unless you throw the ball away while still in the pocket, and since the CPU simply does not do that, and most users don't either, it doesn't really matter.
I've never ever seen a single roughing penalty for either passer or kicker (I guess it's better that way, because honestly, I think you'd get a roughing the passer penalty on every other play in Madden if it were called by the rules), not once an offensive PI, defensive PI I've seen, though, mostly on Mesh plays or crossing slants when you time it that you throw the ball just before the routes cross, sometimes your receiver runs into the crossing defender and you can get the penalty. I don't think defensive PI can be called on a CPU controlled defender who is actually covering the receiver, again it's better that way because you'd get a defensive PI on pretty much every other deep route otherwise.
As the "fake snap" seems to be inexcplicably broken it seems impossible to get an offside penalty save for some weird instances especially in no-huddle situations where the defense doesn't manage to get set correctly because two guys try to get in the same spot, some for encroachment, only attainable by weird positioning bugs (and of course by having the user player cross the LoS), I'd really like for them to adapt the NCAA system for fake snaps/false starts/offside/jumped snaps, seems to work quite fine there.
For KR/
PR interference it's the same, it will get called if you user a player and run into the return guy after he signals for a fair catch, CPU never triggers that penalty.