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There are arguments for/against either approach. My implementation I suspect is very rare.
I would think it depends on the complexity of the modules involved. The core only approach may be useful for modules that bridge other applications (WordPress, MediaWiki, etc). Also would be useful for mature modules which are no longer in development. If the core hook could encompass the system tables (users, configuration, etc) this would open many possibilities.
On the other hand I am sure there are modules with complex data structures, non-database related resources and cascading read/write functionality which may make a module hook a better choice.
Future developments in the core and legacy modules make it tough to say yes or no either way. I encourage other developers to add their 2 cents. For me this is an exciting topic :)