两者没有什么区别，基本上可以换用：

I would prefer that (=I would prefer it if) you did not come thisafternoon. 我倒希望你不要今天下午来。

I’d prefer it if (=I’d prefer that) the bed were a little too long. 我倒希望这床稍大长一点。

I would prefer it if  (=I’dprefer that) you didn't smoke in here. 我希望你不要在这里面吸烟。

I would prefer that (=I would prefer it if) you did not mention myname. 我倒希望你不要提及我的名字。

I’d prefer that (=I’d prefer it if) the job were a little closer tomy home. 我想要是工作离我的家近一些就好了。

请看下面一句摘自《牛津高阶英汉双解词典》第四版的 prefer 词条：

I should prefer that / prefer it if you did not go there alone. 我倒希望你不要一个人去那里。