First, I really encourage you all to learn the strategies of the Pro variant. It's much more about how you play your hand, and much less about just having the best cards from the start. It's much more fun than normal once you realize it's not just chaos, which is what it will seem like at first.
That said, most of the best players on the site play pro, but do not play arena. So it does make sense that arena should be normal I think, as it pleases the majority of people playing there.
The suggestion that these should be two separate games also makes sense. I hope the publisher agrees. As suggested, a different color for the box would work. They might not want to do this because a publisher likes the game to match the real box the game comes in. As a customer who learned the game here, and then purchased a copy of the game, I don't think the box color would confuse potential costomers.