1st: The thing about "rfx" and "fx" is that this is BINARY format thing. BT doesn't have to do anything with it as it operates with middle format data and will never import/export suffixed effect names.
Middle format PIT and PIM shouldn't have "rfx/fx" suffix at all. In the case you find suffixes in PIM/PIT then this files are corrupted!
Hint: PIX converter at current time obviously creates corrupted effect names.
2nd: About in game support of FX in future: 'fx' suffix is translated to 'rfx' when material is loaded in runtime to maintain backwards compatibility.