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I do not known much about fingerprint API for Android/iPhone, but if any external app (on phone) could ask user to authenticate using fingerprint, it may be great if KDEConnect use this api.
Desktop version of KDEConnect should have option to select, which phone may authenticate and user must click on special option in KDEConnect on phone. If desktop send signal to phone, phone KDE Connect will ask user to authenticate by fingerprint and phone send success or error signal to desktop. Simple, huh? Of course, it may be only alternative method.