It sounds like the beef here is really with Qt's handling of alternate keyboard layouts. As I mentioned to someone else, report it and provide the relevant patches upstream to Qt to get this fixed properly.
When Qt patches QTextEdit and the like to properly recognize the AltGr key as separate from the Right-Alt key, it will automatically be incorporated into Sigil. Until then, the only recourse is to change your Sigil-clips shortcuts to something that doesn't stomp on your AltGr defaults.
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