Seen this a million times in panel shops over the years, water gets under the boot rubber, eats out the corner seams...then... boot full of water, might not seem like a big hole but I'd lay odds that's where it's coming from... very very common with cars belonging to people living near beaches or cars used to tow boats.
if the damage isn't too severe you might get away with wire brushing the area and re-sealing with sikaflex urethane sealer/adhesive. goes without saying of course that you'd need to repaint the effected areas
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