Rtabmap exports data in the coordinate frame convention described in
REP103 and
REP105 : x->forward, y->left, z->up.
I am not sure exactly which part of rtabmap-databaseViewer you are referring. On "File->Export 3D Map", you have an option to assemble all point clouds into same file, or export all individual point clouds in their respective file. For both approaches, the point clouds are transformed in map frame. It means that the individually exported point clouds are already transformed in map frame, so that you can open all individual point clouds in CloudCompare or MeshLab and see them next to each other. For "they are not facing just one way, they also face to the side", a screenshot may be helpful.
The map coordinate of each point cloud is determined by the current Graph View's state. The poses shown in that graph are those used to transform the point clouds.
In 3D View, we show the point cloud in base frame (not camera frame), also called as base_link. If Odom checkbox is not checked. If Odom checkbox is checked, we add only Z, roll and pitch to the base frame for visualization. You can right-click and how the Frustum to see the actual camera frame relative to base frame.