There in lays the pitfalls of addins that perform automatic template edits. It may not be hooks doing them, it could be appending data to a template which can not be controlled by this style. What you will need to do is modify the plugin that is doing the template edit and wrap it in conditionals so it doesn;t perform the edits for the mobile style.
If it's an add-on here at vb.org. point me towards it and I'll try and let you know what you need to do...
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