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Seems like with the functionality we have now... adding tokens on different map layers and assigning those layers a 'height' value would allow for layered maps to be used and targeting to work across multiple layers is something that could be added.
I'm sure all of this doesn't 'work' at the moment.. but it seems like something to aspire to.
Note that the developers ask that feature requests be added to the Wish List, so that they can be tracked, searched, sorted and voted on by community members. http://fgapp.idea.informer.com/
That does not mean that a forum post isn't valuable for discussion. I suggest you do both, and place a link in each one to the other so that people vote on the Wish List and discuss here.
But a forum post alone is a poor means since it will soon get lost in the numerous forum threads.