That is the arguable part: some dealers refuse to install
aftermarket tune equipment; or work on cars that have it, threatening that warranty is being risked; other service departments have no issues with either.
This part is down to either a misunderstanding of how warranties work, or just sheer pig-headedness. Remember that unless you're talking about a dealership warranty (ordinarily only a factor after factory warranty has ended), the dealer is only an agent for the manufacturer, and ultimately doesn't have the final say in whether you get a warranty claim approved or not (though they may have some influence).
Adding an
aftermarket item cannot invalidate the entire warranty on the car. All it can do is create cause for consideration as to whether the
aftermarket item contributed to a specific failure on which warranty may be claimed.
As an example, adding an ECS10 control module to your car cannot cause you to be unable to claim warranty on an engine failure due to a failed turbo. Similarily, adding a JB4 piggyback tuner cannot cause you to be unable to claim warranty on your sunroof.
An ECS10, however, could be a consideration in a warranty claim if you had a suspension failure, as that failure could be caused by the dampers operating outside of the factory-specified parameters.
In a different fashion, you cannot claim any warranty from Kia on
aftermarket parts, either directly or indirectly. So if you have an
aftermarket item on the car and a stock part fails and causes damage to that
aftermarket part, you cannot expect Kia to replace your
aftermarket part - only the stock part which has failed.