Learn English – Can we use “although” and “but” together i.e. in one sentence

I would rephrase it as follows:

According to the host, it not only serves to prevent robberies, but also serves to prevent bad spirits from entering.

The sentence is similar to "She not only wrote the text but also selected the illustrations." Notice that not only is written between the subject and the verb.
As others said in comments, as well is not necessary, since the sentence is already using also; using both is probably like writing "She was not only intelligent but also very musical too."

As for using prohibit, the verb is used as "prohibit something," "prohibit somebody from doing something," "prohibit doing something, or "prohibit something/somebody from doing something." In your sentence, prohibit was used as "prohibit somebody" which is not how the verb is normally used.

Your statement looks fine to me, although I have corrected a few unrelated grammatical errors because it helps to make the question clearer. :)

Although in this case is suggesting that an exception to a rule has been made. Here, the implied rule is that a graph representation is expected to be a complete one. It's perfectly reasonable to use because in the clause that explains why the exception has been made. Here's another example, using the recent Kentucky Derby result:

Although California Chrome won without a particularly fast time, this was because Espinoza eased him up at the end to save him for the Preakness.

The "rule" is that you want to run at a time comparable to the other great horses. The exception is that he was running fast enough to win and had another race to run soon.