Hibernate tools aren't just one thing - it depends which part you refer to ?
if for running hibernate queries then yes, right now we can't support all those three in one setup (mainly because of API differences and the time needed to separate out to be independent of the underlying API - its all doable, just need someone to have time to do it).
For the code generation aspects then Hibernate tools output works fine with Hibernate 3.6 and even 4.0.