This article[0] says "Data changes are usually much less frequent than queries, so incurring an initial cost of processing data into an index is a fair price to pay for instant searches afterwards."
Is that what you're referring to with cache replacement? There's no way to quickly update the index?
Wikipedia says "The R-tree was proposed by Antonin Guttman in 1984 and has found significant use in both theoretical and applied contexts."
I'm gathering that there are applications which are ok with that limitation? Generally there is communication and awareness between industry and academia, if everyone really needs cache replacement for it to be useful, why have they not attempted to account for it? What is the cause of the total disconnect you describe?
[0] https://blog.mapbox.com/a-dive-into-spatial-search-algorithm...