That's certainly true. But the implication of his statement is that a sitting President shouldn't be investigated, period. His reasoning for saying they shouldn't be investigated is that it would affect their job performance. A congressional investigation would too. It's a logical jump to assume he doesn't want the president investigated at all.

That said, assuming Congress will investigate seems rather... idealistic? If the sitting President is in legal trouble, their party would want to support them, not investigate them. As we are currently seeing across the country. So what happens when Congress is majority ruled by the same party as the President?