Consider a sentence of the following form:
X, and the Y which comes with it, is good.
Assume X and Y are nouns, and X is singular. Should "is" be replaced with "are"? Is there some other grammatical error I am missing?
It should be "are." The problem is with the commas, which should be left out. You may be thinking of a sentence like "X, as well as the Y which comes with it, is good." In that case only X is the subject, so it takes a singular verb.