Are you using texture repacking at runtime to create new combined atlas textures? Then you could call the following to free up resources:
AtlasUtilities.ClearCache();
Resources.UnloadUnusedAssets();
In general there should be no steady growth of allocated memory when switching to different scenes when skeleton objects are loaded normally.
If memory grows steadily when only using unchanged skins, could you perhaps share a minimal Unity reproduction project that still shows this issue, then we can have a look at it. You can send it as a zip package to contact@esotericsoftware.com, briefly mentioning this forum URL so that we know the context.