Not all parenthetical expressions need to be set off by parentheses (or commas, or what have you). It can be argued that title is the subject of that sentence, and the entire reference to tone is ancillary to it. Moreover, "as well as" doesn't perform quite the same function as the conjunction and. It doesn't make the same kind of list.
James and Horace are friends of mine.
Here it would be wrong to use the singular. "James and Horace is a friend of mine" just doesn't play.
But look at it with the other construction:
James as well as Horace are friends of mine. [?]
James as well as Horace is a friend of mine. [?]
To my ear, Horace is definitely reduced to a supporting, if not exactly insignificant role in the sentence. The subject of the sentence is primarily James, and he must rule the copula. Treating them as equals doesn't feel right to me — otherwise, why not just end the ambiguity with and? Even if you argue that someone might wish to use "as well as" to place rhetorical emphasis on the included subject, as in
My Aunt Betsy as well as the physicist Stephen Hawking believes that black holes will eventually evaporate.
Another problem with your example is the parenthetical expression itself. What is it, exactly? Would you really punctuate it thus?
The title, as well as the tone, of the novel ...
That seems awfully stilted and gracelessly halting. If I were writing that sentence I would prefer to recast the sentence to something like
The title of the novel, as well as its tone, derives from ...
The novel's title, as well as its tone, derives from ...
and if we eliminate the punctuation
The novel's title as well as its tone derives from ...
it still feels better (at least to my ear) to use the singular. The plural
The novel's title as well as its tone derive from ... [?]
simply sounds wrong to me.
Now, having written all this, I have to say I'm not willing to fall on my sword for any of it. Given the choice, I would either take the trouble to use the commas to make the parentheticality (if I can use that word) unequivocal, or else take the coward's way out and avoid the construction altogether.