Take a look at WordPress hooks from the Plugin API. There are actions and filters to be used by plugin authors so that other developers could alter the content without changing the core code. However, if they are not used properly (or missing), the only two options are CSS changes (wherever possible, because stylesheets could override the UI at some cases) and the WordPress API hooks (so that you could manage the content globally from WordPress and rearrange order from calling different functions). Custom requirements usually expect flexible plugins with hooks and therefore the lack of them doesn’t give you any other clean options.
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