There is a legal mandate regarding warranties and what they will and will not cover. It is called the Magnuson-Moss Warranty Act.
In a nut shell, companies that sell "consumer" items are NOT required to offer a warranty. But if they do, their warranty MUST comply with the MMWA.
That being said, a company is not allowed to void the ENTIRE warranty on an item if you modify or change one particular part on the item in question.
Let's use cars for an example as this is the easiest analog. If you replace the headlights on your shiny new ride with super bright blue xenon laser and the excessive current draw from these lights burns out the headlight switch, the manufacturer is not required to honor the warranty for that repair.
In general, the manufacturer is not required to honor any warranty claim if the failure can be shown to be caused by misuse, modification or lack of maintenance.
However, let's say the engine springs a nice oil gusher from the valve cover gasket. Since the odds of your super fancy headlight bulbs causing this failure are zero, the manufacturer must honor the warranty on this component.
This is essentially the same situation with Stern. At least they were nice about it and put out a service bulletin to warn everyone. Stern has already stated that aftermarket shaker motors can damage the node board. So if you install one on your SPIKE equipped pin and it fries the node board Stern is will not honor the warranty on that repair.
On the other hand, if you installed an aftermarket shaker motor and the DMD display failed, well the shaker motor has a very low likelihood of causing a DMD failure so Stern should be obligated to honor the warranty on that repair.
It's pretty simple really.