This is really confusing. So let me get this straight, if we inject our unique code from our rom we personally dumped, into the scene game (of the same size), we'll be able to go online and not get banned?
Nope. Nobody ever said you won't get banned. Although it is possible you are "less likely" to be banned.
It is possible that Nintendo has a database of every header in existence, just like how PC game companies have a database of CD-Keys.
Just because they haven't done anything about it now, doesn't mean they will not in the future.
Even if you were to dump your own ROM, and inject the header into a scene dump of the same title...
Nobody knows for sure if you will get banned or not sometime in the future.
Cheating the system is a dangerous game, whether or not you are willing to take the gamble is up to you.
The first wave of bans will probably happen shortly after a surge of people are caught cheating online, like when Smash Brothers comes out.