Try to think of it as 'the top of the table has the books'.

Location goes before the verb, unless it's a result of the verb.

The main idea always comes lastly

The main idea always comes lastly

No, 有 is more directly translated as "have" so that sentence would be "have two books on the table" which is an incomplete sentence

Yes

It should work, but without 有. With 有, it just doesn't work in this particular case.