Closing as Won't Fix. Loading the JavaScript skin extensions in the iframe-based standalone WYSIWYG editor can't be made safe in general: many modules (e.g. Live Data) inject elements at the end of the BODY, which is the root editable element of the iframe, so they would end up in the saved content.
Instead, the idea is to use the iframe-less CKEditor (the one used by the in-place edit mode) in the standalone WYSIWYG edit mode too, see XWIKI-25433. The configuration then becomes useless and will be deprecated in XWIKI-25434. This also replaces https://github.com/xwiki/xwiki-platform/pull/3797.
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