The Maxim app note explains why they fiddle the address lines- most flash parts need you to access certain addresses in certain sequences to lock/unlock and to program. As far as the processor is concerned the data it writes is the data it gets back even with the fiddled address lines. As for programming the flash device separately - you'll need to fiddle the programming file to cope with the changed address lines.

I don't know of any easy way to achieve this apart from writing a program to do this or manually doing block moves in a hex editor.