Aye, you're right. I don't know if you found this in the Ruby/Sapphire disassembly, but I didn't think to look there until after your post...
I tested with this code in PKHeX (well, a worse version of the code at first):
public bool WishmakerJirachiGiven
{
get => GetFlag(BlockOfs[4] + 0x2B1, 0);
set => SetFlag(BlockOfs[4] + 0x2B1, 0, value);
}
@Kaphotics would you be interested in adding the flag into PKHeX somewhere?