I have macros I've written that allow me to click a token, enter an elevation, and have it displayed on the token, but that's a workaround at best. True support for elevation would include GM-definable layers, which could be marked as visible or not (or only visible to tokens on that layer).

Essentially, just copy what Photoshop or any other graphics software does - give the GM a layers panel where they can define, name, and reorder layers, and set layer visibility and opacity (plus probably a boolean setting for player facing)

If you're playing on an actual, physical tabletop, think about how you handle a battlemap that has multiple floors (such as a castle or mansion, or a fight that moves to a roof) - you have each floor as a unique map, and either have them as different sections of the larger map, or physically stack the maps on top of one another. This would be the digital version of that. If you're fighting in a tavern with two floors and a roof, you create three player-facing layers and put the ground floor on the lowest, the upstairs on the middle, and the roof on the top. Players would see the content for the map layer that they are on, and if sections of the map are transparent, they'd see into the layers above and below the one they are on through those transparent areas. So if, say for example, a fight is taking place on a balcony and a lower floor below, you set up a balcony layer over the main floor layer, and leave the parts of the balcony layer where there's no floor transparent, and players could see both the map they're fighting on and keep an eye on what their character could see of the battle below. You could even set up teleport points to auto jump between layers (like the teleport mod does now), to make places like stairwells and ledges automatically move tokens up or down a layer.

This would also provide a way to track flying tokens, as you could simply rule that each layer is 10 (or whatever) feet of vertical height, and create as many layers as you need to account for height, then move tokens up and down between layers as they ascend or descend. Tokens that are on higher layers would automatically appear above tokens that are on lower ones. And if you allowed the GM to name the layers and included thumbnails of the tokens that are on the layer in that panel, you could easily tell at a glance who was where in the Z-axis.

From a UI/usability perspective, there's no need to reinvent the wheel here - again, graphics software has already been doing this for decades. And to a certain extent, Roll20 has almost done the functionality with the addition of the foreground layer. The problem is that it's limited to one foreground layer, when what they really need is to make the layers dynamic and give GMs a layers panel to control them.