It’s not a case of mutual exclusivity. If a story is about a particular place it can very well be set in that place.
Sure, but I think now we're mixing up 'story' with 'theme'. Normally this really wouldn't matter (Matterhorn & Space Mountain have themes, but no real story - and that's ok!) But because AK has ...thus far... been very consistent with its subject matter, the stories of possible new additions to the park are being heavily scrutinized.
And all of this is besides the point because not only does Indy fit the style of AK, Indy CAN have a story that supports the AK subject matter of Nature > Man.