Layers will be conceptual (i.e. the GMaps API does not know about layers), but yes. You can store markers added to your own layer array. Each member of this array will be an array of markers corresponding to each type. You can create your own markers, create them anywhere on the map, etc.
The API may be too slow for a game in which markers move in real time, depending on the rotation, this is certainly possible.
What you cannot do is copy the image and redistribute it so that your game can work on top of Google Maps.
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