The plugin has been updated, this should no longer be an issue! The mouse cursor should be located above ALL elements on screen at all times from now on. This should also include external DOM objects that are attached by external plugins. :)
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I'm sure your changes have helped others, thank you for that. My own problem appears to be an incompatibility issue with OcRam's Passages plugin. If a tall character approaches a (for example) chest from the south and the mouse hovers over where the chest is (now covered by the torso of a taller sprite), the mouse cursor does not change. I'll have to take a look at what's not playing together nicely.