Great question.
I like the Ki-64, but the cooling system on the only prototype eventually failed and the aircraft caught fire. Not the best recommendation, is it?
They actually made 6 VB-10s, and that alone says the VB-10 was more successful. But, then again, it didn't fly until after VE day, so it wasn't a wartime combat aircraft, although the design certainly was. Both had about the same speed, but the Ki-46 cilmbed at least 50% better, likely due to much lower weight (13,000 pounds versus 20,000 pounds with about the same horsepower in the engines).
I'd say both would have required some teething trouble solutions had jets not come along when they did, but I prefer more power in a fighter and have to go with the Ki-64. Likely, both would have been about as good or bad, as the case may be, as the other one had they made it into service. After the war was over, rate of climb was a non-factor anyway.
Both likely would have caused their respective crew chiefs no end of stress as burried and coupled engines are NOT easy to work on. Heck, the Allisons in a P-38 are not easy to work on, either and likely have about the same access as the coupled engine, so maybe it wasn't going to be a real factor. Changing a rear engine would have been a real bear! So, I'd bet the pilots would have feathered the rear engine prop and cruised on the front one ... maybe. Pilots back then were many times notoriously inconsiderate of the woes of a mechanic, unless the mechanic had liquor on hand most of the time.
Go watch Baa Baa Black Sheep and tell me it ain't so!