Hello Dukytony,
Mission planner feature in Metashape is designed for image acquisition of the structure with the complex shape (mostly we have been thinking about buildings), so if you are interested in common nadir aerial survey, you might need to consider a different mission planning application focused on such types of the surveys.
As for the 99 waypoint limitation, the latest version of Metashape generates now the single mission plan (camera track) which can be split into parts with the user-defined waypoint number upon export.