朋友,我觉得你是想多了,seem是系动词,后面的从句当然是表语从句.
比如我说,It seems that you're quite confused with this sentence. 换句话说就是 You seem to be quite confused with this sentence.
It's ... that ...是一个固定的搭配 当然 it 后面的系动词未必是is.从你的问题来看,这一点你应该清楚的.
个人观点,仅供参考啦.而且这种问题上也不必过于纠结.