grammar - Not only X but also Y are (is?)

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.