This system does not seem fair, at least as it appears on paper.
能否理解为：This system does not seem fair, at least as it appears on paper （that this system does not seem fair）.其中as=that this system does not seem fair.
不过又感觉这么理解不妥，由于根据某种说法（曹老师过去说过），as it appears……中的形式主语it不可以单独出现，需要和逻辑主语（that this system does not seem fair）同时省略。（也会是我对曹老师的解说理解不到位，在这里进行了错误的类推。曹老师的解说原文：比如：The difficulties are even greater than appears at first sight.……假如省略that从句，形式主语it需要同时省略。）
很期盼老师的指点。
appear可以是出现、呈现的意思，也可以是好像，表面上看起来的意思。
曹老师说的 as it appears that +从句这个句型。as引导比较分句为这种句型时，假如省略that从句，it就需要同时省略。此时的appears为好像，表面看起来的意思。
但你的句子中，appear是出现、呈现的意思。it为人称代词指代this system。和曹老师说的完全不是一回事。as在此引导方法状语从句，可以用the way替换。
This system does not seem fair, at least as it appears on paper.
This system does not seem fair, at leastthe wayit appears on paper.
这个体制不公平，至少从文件上看是这样。
