I understand why the Starry Sept would have become the center of the Faith eventually, but there was a period of 300 years when the Vale was all the Andals had, then came the conquest of the Riverlands, and the Andals didn’t come to the Reach until “generations had passed” since the conquest of the Riverlands.
In that intervening period, you’re going to get a major center of faith in the Vale. There’s no way the Arryns aren’t going to use some of that Vale to raise up a Sept to glorify Ser Artys Arryn and his gods-ordained victory over the First Men, and by extension to emphasize their authority over the lesser Andal kings of the Riverlands. And with hundreds of years of pilgrimages and donations from guilty-conscienced knights and lords looking to buy their way into Heaven, that Sept is going to be very, very fancy and the Septon who runs it is unlikely to tug their forelock to some lackey of the Hightowers without a fight.