For one thing, I don't think their JIT produces code that properly follows the Windows x64 ABI yet. It really should be disabled in 64-bit builds until they do.
Following the ABI is only an issue at module boundaries. If you control every callsite of a function, you can invent whatever calling convention you want.
But you still need the function tables and follow prolog/epilog conventions with x64 for SEH to work.
Their stated reason for de-prioritizing 64-bit builds wasn't technical; rather they say they don't have the manpower to do both. Perhaps the manpower issue is that they don't have enough people to work on the JIT issues on x64 and do everything else, but I do not believe they specified.