That's funny. To me separating the verb from "not" feels wrong, because if someone tells me "They are the same", I could answer: "No, they are not!". But I think both are correct. I think you could pretty much put "however" anywhere in the sentence and it would still be correct. It just changes the stress in the sentence.
However, they are not the same. They, however, are not the same. They are, however, not the same. They are not, however, the same. They are not the same, however.
I think it is context and personal preference that will dictate which one to use.
A very old question but I'll give it a go anyway:
In English you can't usually use adjectives as noun arbitrarily. For instance in English you can say "the tall one is my brother" but not "the tall is my brother", that sounds awkward. In romance languages however it's usually fine.
I'm guessing that part of the reason is that in Portuguese and other romance languages both "the" and the adjective inflect depending on the gender and number, so it's a little less ambiguous. In English "the tall" could be singular, plurial and used for any gender. In Portuguese you'd use o/a/os/as with the correct adjective inflection, so you have more meaning with fewer words.