Modding my bike is perfectly legal, after all, I bought it. But you really think Harley Davidson is going to warranty repair my S&S engine ? Or revalve my progression suspension if it gives out ? No, the 3rd parties will, but it's their parts.
Heck, if I install a 3rd party air cleaner, or even Harley's own but don't follow their guidelines of flashing the ECU with a stage 1 download, you think they'll warranty the snapped rod or cracked piston sleeve from the detonation that occurred after a lean condition ? Of course they won't.
Warranties are there for manufacturing defects. If you dick around with the device, you're going to have to take the company to court to get warranty repairs. Magnusson-Moss unfortunately doesn't work with magic, it works with courts and lawyer fees. And you're not garanteed to win because let's face it, your mod might just be responsible for your trouble.
I wondered about what other industries do. Auto industry, for example. If you put an after market FI chip in the fuel injection computer, is the engine still warrantied? I'd think not, the manufacturer can't support something that modifies the expected engine function. That seems totally reasonable. Just because software is inherently flaky stuff doesn't mean companies should support every variation of it.