Since you're using the auto-tuned index for FLANN it's going to build a large number of indexes to try and find the best performing one, which can take a long time. Properly tuned I would expect FLANN to be much faster (though that's expected since it doesn't do exact searches). Also benchmarking the index build time together with query times doesn't make sense to me since depending on the application you may not care how long it takes to build the index.
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Since you're using the auto-tuned index for FLANN it's going to build a large number of indexes to try and find the best performing one, which can take a long time. Properly tuned I would expect FLANN to be much faster (though that's expected since it doesn't do exact searches). Also benchmarking the index build time together with query times doesn't make sense to me since depending on the application you may not care how long it takes to build the index.