Not only X but also Y are (is?)
The correct word should be is.
You wouldn't normally say "a book are on the table" or "a pencil are on the table". Since you did not make a list of nouns or use any plural nouns, the verb should remain singular.
Regarding your second question, you have now changed the focus from singular to plural.
In your first example it was "Not only X, but also a Y is on the table." The focus is on Y. But in your second example it is "An X, and also a Y, are on the table." The focus is on X+Y.
So yes, in that situation, "are" is the correct word to use.