"How come" (a common alternant to "why" in informal speech) is best regarded as a compound interrogative word functioning as an adjunct in clause structure.
Exceptionally for an interrogative, it doesn't trigger subject-auxiliary inversion, thus
How come you are sitting here ...
is the correct structure.
The idiom "how come" ...
This article explains some of the background to the set phrase how come. The article suggests that the set phrase might be an abbreviation of "How did it come about that..."
Yes, you can use it with sentences containing auxiliary verbs. It's OK with modals as well:
How come you must do your homework tonight, when you don't have school tomorrow?
The simplified form of your sentence is as follows:
The purpose is how to acquire X
This means "the purpose" is the way or method to acquire X. A purpose is normally a reason and not a method of doing something, so this sounds strange.
The purpose is to acquire X
This is answering the question "what is the purpose?" - so here we are ...