@Chris thanks for those answers about area calculation

@margusl, the data I posted were just an example of a recurring problem I had when doing spatial analysis with multipolygons, many time I have experienced invalid geometries that are not always fixed ST_makevalid() or that need to be simplified for speed, but even simplifying doesn't always work.

My final goal is being able to see how much area of say seagrass is within each countries national waters, so an overlap between habitat and EEZ. Or see areas where seagrass overlaps saltmarshes, or the distance between these ecosystems. So often I will need to have the attributes of both original polygons. I might need to intersect more than 2 polygons. Does that answer your questions? I didn't realize that even within a shapefile there were overlapping polygons.

@pieter and @Ian, thank you for the suggestions. I will keep in mind but a bit hesitant to invest in new tools as there's a learning curve.