It does sound strange, but people using this method, myself included have not been banned, and people using online headers have been banned, so you can argue the logic of it, but the fact remains, personalized headers don't get banned.
Whether Nintendo can detect mismatched headers is something that no one knows, or will ever know since Nintendo won't disclose, so you might as well stick with something thats proven to work.
As for Nintendo banning private headers, one game can only go online at one time. So as far as Nintendo is concerned no matter how many games you use with your private header, you will only ever be online with the header once at a time, so it becomes much harder to flag.
This is Nintendo's method of weeding out false positives. If someone dumps a header and makes it public then sells the cartridge, then of all the the people that are being banned, there will be one person who is a false positive. This person should own the original cartridge that the flagged header belongs to and should be able to provide Nintendo a image of the cartidge ID that the flagged header belongs to to. In this case, this one person will be removed from the ban list.
