The Act serves to outline what can and cannot be stated in a warranty. This butt right up against other laws that do as mention in the OP's post. That is, if a warranty states X is covered under the warranty but Y was modified, as long as Y did not cause X to fail, then X is covered under the warranty. The MM Act places guidelines on the warranty that don't allow it to include an exclusion against X being covered even if Y fails.This act protects you if you use non-manufacturer's replacement parts such as filters, sparkplugs, belts, tires, oil, wiper blades, mufflers, mounts, brake pads, etc. It does not mean you can alter the vehicle and expect the manufacturer to repair it under warranty.
The Act does also allow consumers to use non-OEM parts without voiding the warranty (unless the party offering the warranty pays for the OEM parts). Again, this carries over to adding an AM part without it automatically voiding the warranty _just_ because it's AM and not OEM. But yes, the warranty can still exclude a loss if it can be shown that the AM caused the damage. Then there are different laws/rules that apply.