I look at this as a positive and not a negative. Shenmue III is being made on a shoestring budget as it is. If You Suzuki wants to maximize profit on each game sold, then this is a smart move. Valve takes a 30% cut, Epic Games would also take a small percentage cut as well for using Unreal Engine 4. Epic Game Store only takes a 12% cut, plus there is an extra incentive with UE4 where they do not have to pay any royalties by selling the game on EGS.
Shenmue III isn't going to be the ending of the series. It is just chapter 3 on what will be more than likely a 4 chapter game series. If Yu Suzuki wants to get the ball rolling on Shenmue IV while funding his studio, it's not so bad that he wants to make as much money on each copy sold, as possible.