That's a tough one, but this one requires some technological knowledge to figure this one out. Anyway... Here goes!
The Action Replay is a hacking device, enabling you to do and get things you can't playing the game normally. But the encoding in the game, aka programming, NOT the hacked encoding (AR), is built to conform with what is intended. So, for example, take Wario's woods. This is something you are supposed to get, designed for GBA use. But, Zelda, being a hacked game, is not built nor intended for GBA use.
Whew...... I hope you read this! ;)
Groon