The TFS heads do have a +.300" raised stand pad in comparison to factory and "normal" aftermarket FE heads. However, the valves are .050" longer (5.500" OAL vs around 5.450"), so the actual net difference is +.250".
What we run into is that different rocker arm systems interface with the TFS heads differently (just like they do with other heads). Sometimes they will just sit right on without any work (like the Harland Sharp setup), sometimes the stands need a lot whacked off (T&D's and factory non-adjustable/adjustable stands need ~.200" cut off), and sometimes they just need about .100" cut off.
What Rory is seeing is probably more typical than not.
My approach to this, if a universal stand was to be made, would be to make them .200" short and then just shim up as needed. Otherwise there would have to be several different heights to work with different rockers.