Dragonite has nothing to do with Lance or the final gym, so there is no problem with gameplay, although you can't get to Mewtwo. The Dragonite does not need to be interacted with, it interacts with you when you have seven badges.
In earlier versions of Glazed, Dig was required to access Blackthorn City. In the most recent version, I realized this was silly, and required the trainer to give Dig, not a great move, to a party member, for one singular obstacle. Thus, I made Ice Cave permanently open; Blackthorn Gym still cannot be accessed until seven badges are obtained.