Very few people remember that the underwater base wasn't the Decepticons original ship anyway, and the physical similarities were debated all the way back on Ben Yee's old discussion board, with the usual head-canon being that the Decepticons used either parts for or blueprints from their first ship to make things work, so a base mode makes sense. Extending tower gimmick?
I'd not be surprised if the Purple Griffon did make an appearance, simply because it exists and would have a hard time fitting anywhere else, like how Countdown wound up with Omega's big rocket. Besides, it's not the first time we saw a 'beast' counterpart to the Autobot city/base. Metroplex with Trypticon was obvious but Fort Max had 1/3 of Skorponok too...