Gene, 

there are situations in which 'why' and 'how is it that', and ' how come ' may be interchangeable, but they are not identical in all cases in English. The same is true for 'pourquoi', 'comment ça se fait' and 'comment se fait-il que ...' in French.  

Languages regularly have more than one way to express the same idea and closely related expressions that carry nuance. Some of this is 'aesthetic' and some functional. 

It is also true that the subtleties of one language's expressions can easily be lost trying to translate simply and directly into another language's expressions.

 

The following examples do not ask the same question twice in either English or French :

Why are we here? How is it that we are here ?

Pourquoi sommes-nous ici ? Comment se fait-il que nous soyons ici ? 

Ultimately, whether choosing to use these phrases or not, they are used in French orally and in writing, so it is at least worthwhile knowing them. 

Both languages have an informal and formal expression here - so immediately that introduces 4 expressions to consider. It is a B2 topic - some level of complexity is to be expected. 

I will leave it with the Kwiziq team to follow up on whether it can be simplified or presented better.