Both Mario Artist: Paint Studio and Mario Artist: Communication Kit were intended to support the Game Boy Printer via the 64GB cable, a peripheral which was showcased at Spaceworld 1999 but ultimately shelved. Within the data of both games are code that reveals an otherwise hidden "Pocket Printer" icon if they detect that the cable is plugged in. Selecting this opens a menu where the player can print out images of their creations in one of multiple different configurations. Interestingly, one of these options allows players to print images in color despite the fact that the Game Boy Printer only permits black and white printing. As Nintendo never officially announced a color version of the device, this indicates that one was being developed before being cancelled as well.

Within an early build of the game recovered from a Nintendo 64DD development disk is a remake of the "Gnat Attack" minigame from Mario Paint. The build is dated to February 11, 1999; as the game itself released almost nine months later, this indicates that this iteration of "Gnat Attack" was cut fairly late into development. The N64DD version differs from its SNES counterpart in its use of fully 3D environments, one of which features a TV displaying the title screen from Super Mario 64. After the player completes a full loop of the four stages available, a medal appears in the bottom-left corner of the screen and the next loop becomes more difficult. After five loops, the game resets to its initial difficulty; beating it a sixth time crashes it. Additionally, there are unique graphics for four other medals, while in normal gameplay, the first medal is replicated each time the player finishes a loop. These features imply that "Gnat Attack" was not completely coded at this point in development.