I think in a round-about way, they could lead to problems that would be the result of adding them. For example: not all cars require PCM tuning in order to run long tubes (I'm assuming you mean long tubes LTs)) however so do because they'll over-compansate with to much fuel or won't compansate enough. Each of those conditions can result in different things and failures. Okay, I'll tune the PCM - no biggie. Well, I think if you get into the PCM (unless it's through a GMPP-specific flash program (which I have not heard or ever seen anything about)) you'll be changing parameters that GM has set when programming the car and therefore void your powertrain warranty. I don't see any othe headers being offered by GM except shorties, in order to remain CARB-legal (unless they don't consider them accessories and as performance parts) and if that's the case you probably won't need much tuning because shorties have not really given much performance gains over LTs in the past because they didn't effect exhaust flow as much as LTs.
Sorry so long... The cam will - without a doubt in my mind (regardless of OEM or aftermarket) but I think you'll be asking for trouble, if you're worried about a warranty, unless you use anything outside of GMPP.
"...What IS true: We anticipated that this would happen - we are never finished - and yes, Ford DOES deserve to win now and then. To think that GM can come out with a car to make ford throw in the towel is simply foolhardy..." - fbodfather