The issue likely isn't just jQuery, we also require Bootstrap's javascript. Unfortunately, template developers, extension developers and any other piece of code that can get your site can include their own versions of each of those files. Our "Include jQuery / Bootstrap" option does include a namespaced version of those files. The benefit is that there is no way the can conflict with the other jQuery's and Bootstraps on your site and no other versions can conflict with ours. But, you're correct, it's an extra inclusion of a file that even we'd like to not have to include.
Unfortunately, there's not a way to fix this reliably other than to include ours. The jQuery and Bootstrap versions we are compatible with are the ones that ship with Joomla. If those versions are being used by other extensions or they are loading Joomla's versions, then you shouldn't need our "Include jQuery / Bootstrap" setting. If you're site is loading newer versions, which have incompatibilities with the older versions (like you mention), you'll need to load our compatibility layer.
Joomla 4 brings jQuery up to date and decouples things better. We're very excited about the opportunities there.
I hope that helps explain,
Alex
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