The parallelism rule doesn't say that everything that satisfies the rule is correct and nice: it just says that everything that does not satisfy the rule is wrong.
You can divide a sentence up in lots of different ways so that each clause contains the same grammatical components:
1) Tom not only has friends in America but also has friends in Canada.
2) Tom has friends not only in America but also in Canada.
3) Tom has friends in not only America but Canada.
All of these satisfy the rule: not all of them are equally nice. For me, the second example sounds nicest so that's the one that I would use.