If every question in JEE Advanced is difficult and different from what is in books, how do average students crack it with a lot of practice?

I will break your questions in parts to answer it.

every question in JEE Advanced is difficult

Well, that's incorrect. Since JEE 2013, they have made it a point that 10% of the JEE paper will be made in a way that even those who have studied properly for board exams will be able to do it.
Moreover, a large part of JEE paper is really doable, and every year people indeed do it!

different from what is in books

Are you joking?
JEE has a well defined syllabus and almost all the standard books available in the market cover the syllabus. Give me 1 example of a question which you did not find in ANY book and I will edit my answer accordingly.
In fact, they lift up questions directly from books.
Which books? The books you ignore - NCERT text books.
Now pick up JEE 2013 paper and sit with NCERT and then compare them side by side. Every concept asked in the paper can be found in NCERT text books. Its all about correct assembly of concepts in a question.

Coming to the important part of your question

how do average students crack it with a lot of practice?

Your question contains the answer. They crack it with a lot of practice indeed!
They solve endless questions so that they develop a directed thinking attitude. An attitude which helps them to analyse the problem and to identify the hidden concept involve.
This attitude is not inherent. This attitude has to be developed.
There is no shortcut.
How to develop it? Read below

In general, a JEE aspirant has 2 years
2 years = 365 x 2 = 730 days
Assuming that you are in no mood of studying for more than 5 hours a day, you have a total of 730 x 5 = 3650 hours
Now you roughly have 90 chapters to be done (30 in each subject)
that leaves 3650 / 90 hours ~ 40 hours per chapter.
Now pick up a chapter at which you are weak and do this:
Study theory for 10 hours
Solve easy problems for 5 hours
Solve medium problems for 10 hours
Solve hard problems for 15 hours
That completes your 40 hours.
Come back to me and tell me your status.

Was that a bit more theoretical?

Well, this is what distinguishes a JEE top ranker from a JEE dreamer.
They apply this theory into practice and do it.

5 hours a day is pretty easy to get, provided you have enough motivation.
People think that you have to sacrifice everything for JEE, blah blah blah.
5 hours a day is no sacrifice! And trust me, its totally worth. Come to IIT and you will realize!

Go ahead and apply it and become a topper.
My best wishes to you :)