We saw a similar example a few years ago in XBLA games. Doom 2 was rereleased on XBLA, however it had an extra episode tacked on (
http://gbatemp.net/threads/a-bit-of-doom-2-xbla-hacking.229989/ for the thread here, there are better ones elsewhere). This technically meant that doom 2 got a new episode officially made for it, quality of such things relative to it and what the modding scene had cooked up since (and
John Romero himself said they did good stuff) is a discussion for another time. What this would be doing is not a lot different to ripping that extra and giving it away -- technically trivial but not a good thing to do under various legal systems. There might be an argument on when the copyright started but given a significant chunk of us will probably not live to see the end of the former (
http://www.copyright.gov/title17/92chap3.html#302 "Copyright in a work created on or after January 1, 1978, subsists from its creation and, except as provided by the following subsections, endures for a term consisting of the life of the author and 70 years after the author's death... In the case of an anonymous work, a pseudonymous work, or a work made for hire, the copyright endures for a term of 95 years from the year of its first publication, or a term of 120 years from the year of its creation, whichever expires first.") that is something of a moot point.
If it was a flag in the game then this discussion would not have happened. If it was data was reshuffled (and then a flag) then yeah the more advanced patching systems would be in play.
The saves stuff for the original GBA release was perhaps tolerated for the original out of maybe ignorance and because loss would be hard to prove (it was Japan only and the ereader device did not even sell in Europe). This is a clear cut difference with an actively sold item, possibly even with this an extra selling point (do I get a game of the year edition because I got the original?), on a current console.
Yes it opens up a whole raft of questions like what I can do about remaking levels, sticking trademarked or copyrighted works into other games and could go further again (we have seen subtitle sites come under fire before for making and translating subs for films and TV, traditional ROM hacking translation is just a bit more difficult version of the same). However this is less fodder for intellectual debate among fans of law and more straight up, out and out, flagrant infringement of an actively sold work from a lawyer happy company -- don't poke the bear is a good policy in life.