These are all the known differences that affect the in-game world. These items come from Disney's Magical Quest Starring Mickey and Minnie on Game Boy Advance that you would normally send through a link-cable. (Or you can get a blank save file with all gba link bonus items already on it through the discord)

Stool ~ A stool will appear in both the Hole Room and the Library, allowing you to get the keys without performing the relevant tricks. (the only difference in GBA Link Any%, saves a few seconds, more useful in GBA Link 100%)

Broom ~ A broom will appear on the Clock Tower Balcony, letting you traverse between the Balcony and the Clock Tower Roof without performing the Gear sequence. (this is a huge time save, almost 3 minutes compared to normal runs!)

Star Container 1 ~ The gold star outside the window in the Wooden Hallway will be replaced with a Star Container. (used in GBA Link 100%, replaces Crazy Hallway SC)

Question Mark ~ Unlocks the Bonus Room from the file select screen. Potentially does something else?

Star Container 2 ~ A Star Container will appear at the bottom of the Bell Tower Interior. (used in GBA Link 100%, replaces the Clock Tower SC)

Note: Extra Star Containers do count towards your total of 12 required for 100%, but will not increase your star container count past 12, which is why you can skip two SCs in GBA Link 100%. Refer to the routing doc for more info!