Thinking about it, Charlie technically has two things seen in other Dungeons, primarily the London one. The boat ride and the elevator. It’s possible they could reverse the boat ride and instead you enter via what was the exit for Charlie and then they use the elevators to represent the descent part of London’s Dungeon.
If they can reroute the queue to go straight to the elevators, they wouldn't even need to reverse the boat section. If I remember rightly, the ride system continued beyond the disembarkation platform on CatCF, following the route Toyland Tours took.
The more I think about it, the more I can see this going into the Charlie building. The Towers would be the perfect location, but quite limiting in what it could do and offer. I could be proved wrong, as the Warwick Dungeon is great, one of the best themed ones. But for Alton I think they'd want a little more, and a boat ride would add to the experience. Who knows, we may see a completely different approach where it is just a boat ride with the Dungeons name.