When becoming a Pentair Authorized Warranty Center, you are contracted to work on warranty work, regardless of where the unit was purchased for. The Warranty Center's cannot charge extra fees, or decline warranty work based upon where the item was purchased. This is a very common thing for shady repair centers to do to get extra money out of the consumer.
Call Pentair directly and they will make sure you get taken care of, if you have any problems with the warranty centers, make sure you contact Pentair back and direct these concerns to them. Pentair pays these centers a fee to do warranty work, unfortunately, some of these centers will try to make extra money off the unknowing consumer. Also, there isn't an authorized Pentair dealer program. If you buy it brand new, it will be covered under the manufacturer's warranty. There is an authorized builder program that allows new pools to get extended warranty if they purchase so many Pentair products however.
Hopefully this help clears this up. I have seen numerous bad companies rip consumers off for warranty repairs over the years.