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I can't speak to the issue of planning in a large area, but the first issue you raise is a good one. You have hit on the problem with explore using its internal costmap while gmapping is creating and correcting its own.

So, explore generates a goal by looking at what the planner cost would be using its internal map (among other costs), but I think move_base is trying to plan using the gmapping map. If the goal sent using the explore map is unachievable in the gmapping map, then you will have a planner failure.

Ideally, you would want SLAM corrections to propogate back to the explore node so that everything is consistent in goal generation and path planning.

I haven't tested how this would work (yet), but I think if you subscribe to an OccupancyGrid message (/map), you can create/update a Costmap2DROS map, and update the explore costmap on the fly.