Using SHI4 for noun and adjective, exceptional rules I have noted the confusion for using "SHI4" and too struggle to grasp the difference.

Common rule for learners is that Noun + Adjective is never linked with "SHI4". As in "He is tall" etc.

However, I have also read (though only in one resource) that for facts and undisputable truth, such as colors, we do need to use "SHI4".

In a comment on a related question here, the author mentiones that for comments about subject/topic, this is commonly used. But isnt it always a comment?

Which is the reason then for "Sky is blue" being translayed with "SHI4" instead of "HEN3". Could it the be translated that way?
It is much easier if you know how your own mother language works, instead of trying to understand "grammar logic" of foreign language with your own understanding. 

Let's look at some example : 

the sky [is] blue ：天空[是]蓝(色)的
the sky [is] crystal blue : 天空是透蓝的 
The air [is] bad : 空气[很]差/坏
he [is] bad : 他[很]坏.  他[是]个坏人. 他[很]差劲
he [is] naughty : 他[很]顽皮
he [is] (a) bad guy : 他[是] (个) 坏蛋/坏人


If you think the confusion is cause by mandarin connector, it is half true. 

I.e., the sentence The air is bad carry out (ambiguous) relative comparison . Mandarin use 很 to explicit brought out relative comparison attributes.  

So He is tall , is relative. It carry out additional comparison message e.g. "He is tall, compare to his sibling".  他很高，和他兄弟姐妹比较的话。

是 used for affirmative, or agree  

He is (a) USA citizen 他是(个)美国人
His lucky charm is a penguin 他的幸运物是只企鹅


Now ，I think you shouldn't have trouble differentiate this : 

他的皮肤很黑

他的皮肤是黑色的


If you use both affirmative 是 and 很, it just emphasize 很, nothing conclusive, but just agree others about something. 

最近生意是很差 （Recently, the business is really bad )
(well, the business is really bad, last time one used to make $1000 a day, now only take home $990 a day, really bad.)  




So in a conversation : 

Lee : The business is bad
李 ： 生意很差
Business partner : Yupe, the business is bad， but it is not doom
生意伙伴 ：生意是很差, 不过还没那么坏


In short, you use 是 if agree on another person relative statement.
X : he is tall    他很高 
Y : yes, he is really tall compare to his sibling,  是呀， 他是很高, 和他家的兄弟姐妹比较的话。 

However, sometime you will prefer to use really 真的 ， as agreement or emphasize your statement. 

He is really tall , 他真的很高