It's sort of complicated. On 3DS, every game has to be programmed to understand the depth slider and adjust the projection by rendering things from different perspectives based on the slider position. In a stunning lack of foresight from Nintendo, Virtual Boy games were not programmed to handle the 3DS slider and there's nothing that can be done about that. In 3DS games, the depth slider is adjusting the distance between the nearest and furthest parts of the 3D image, but you can't do that on Virtual Boy where all the depths are pre-programmed.
Let's take a step back for a moment and look at 2D games. Nintendo officially released Game Boy and Game Boy Color titles via Virtual Console on the 3DS. If you hold Start or Select while booting a Game Boy (Color) VC, the console puts the border of an original Game Boy around the screen and in a 3D depth sense, moves the emulated Game Boy screen back slightly so it sits "below" the border (further away from the player) in the stereoscopic image. Game Boy games don't have to understand the depth slider to make that work, instead the emulator is responding to the depth slider by moving where that flat 2D screen is positioned.
Coming back to the Virtual Boy, that's also what Red Viper is doing. It can move the entire image forward or back, but the emulated game doesn't "know" anything about the 3D depth and is not adjusting to make far away things look further or close things look closer. The actual depth--the distance between the closest and furthest objects relative to each other--remains the same at all times, but using the slider, you're able to configure where in 3D space that image sits to make the whole thing closer or further away from you.
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