RecursivePrefixTreeFilter has some bugs that can occur when searching indexed shapes. One bug is an unpositioned termsEnum. It through an exception in testing; I'm not sure what its effects would be in production. The other couple bugs are hard to describe here but were rare to occur in extensive testing. The effects were probably a slim chance of matching an indexed shape near the query shape. And SpatialPrefixTree does not support an indexed shape that covers the entire globe.
These bugs were discovered during development of tests for RPTF
LUCENE-4419 which I will submit shortly.