It's amazing to me how much misinformation persists about "voiding a warranty". From 40+ years in the car business, I can tell you this:
First off, a dealer can't void your warranty. The warranty is extended by the manufacturer, and only the manufacturer can void your warranty. In all my years, I have never seen a warranty completely voided. I have seen a handful of cases where the powertrain warranty was voided, and those cases were after severe racing abuse was discovered. The dealer provided proof of abuse to the manufacturer and the manufacturer voided the powertrain warranty. The rest of the vehicle warranty was still intact. I have seen cases where a flood car had its warranty voided.
In your case, IF the installation of halos and LEDs caused an electrical issue, and IF the halos and LEDs could be proven to be the cause of the issue, then that particular repair would not be covered under warranty. On the other hand, it is highly unlikely that the halos could cause a wheel bearing to go out, so that repair could not be denied under warranty because of the halos. In other words, if the halos caused a problem, that problem would not be covered under warranty.
Same goes with the Flows and exhaust tips. It would have to be proven that they caused a failure before the repair of the failure could be denied under warranty.
By the same token, if you put a blower on your engine, you would probably lose your powertrain warranty, since the blower puts additional stress not only on the engine, but on the transmission, rear end and axles as well. Don't look for a warranty claim to be honored on any of those components. But a power window motor would be covered, since there's no way a supercharger can cause a power window motor to fail.
By intake, I'm assuming you mean CAI? The dealer would be hard pressed to deny a warranty claim based on a CAI, especially if it's a Mopar-branded unit. He would have to show that the failure was attributed to the installation of the CAI, and that would be a hard case to make.
The best thing you can do is be on good terms with your dealer. If worse comes to worse, you want him in your corner. He's the one in contact with the manufacturer and he can be an ally if he's on your side.