WordPress has quite narrow expectation for plugin directory structure. It is tightly coupled with loading process and API functions.
While I know attempts have been made to make it more flexible, I am not aware of any real breakthroughs or mainstream adoption.
As of current state of core I would estimate you would waste more time trying to implement it, than save time benefiting from more elaborate folder structure. Personally I make any “groups” of plugins or theme and plugins on IDE projects level.
For trivia themes on other hand are much more flexible in this regard and core allows to register arbitrary additional directories containing them.
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