Hope you are having a fantastic week. I'll jump straight to the topic.
I'm using xfce-Kali 2020.1b, xfce v4.14.
I wanted to assign 'Super' to xfce4-appfinder in place of whiskermenu because it was way more responsive on my chromebook machine. I was able to bind it and use xfce4-appfinder but was unable to disable whiskermenu's shortcut. So they would launch at the same time or one after the other.
As far as I understand, whiskermenu used to only launch with a keybind to xfce4-popup-whiskermenu that could be set via the Keyboard app's application shortcuts section. But that caused issues with being unable to use 'Super' for any other shortcut because the shortcuts set in "~/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-keyboard-shortcuts.xml" still get activated on press rather then on release as stated here in the xfce's bug tracker. But I don't have this problem. So my best guess is Super was hard coded to whiskermenu by some party to remedy this bug.
I did a grep search on the entire machine to find where the cfg file for this hardcoded Super is but was unsuccessful. All I found was Ctrl+Esc shortcuts, which cause no harm:
$ sudo grep -ri "xfce4-popup-whiskermenu" /* 2>/dev/null
/etc/xdg/xfce4/xfconf/xfce-perchannel-xml/xfce4-keyboard-shortcuts.xml: <property name="<Alt>F1" type="string" value="xfce4-popup-whiskermenu --pointer"/>
/etc/xdg/xfce4/xfconf/xfce-perchannel-xml/xfce4-keyboard-shortcuts.xml: <property name="<Primary>Escape" type="string" value="xfce4-popup-whiskermenu"/>
Binary file /home/thmyris/.mozilla/firefox/gzthh3eo.default-esr/places.sqlite-wal matches
Binary file /home/thmyris/.mozilla/firefox/gzthh3eo.default-esr/places.sqlite matches
/home/thmyris/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-keyboard-shortcuts.xml: <property name="<Primary>Escape" type="string" value="xfce4-popup-whiskermenu"/>
/home/thmyris/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-keyboard-shortcuts.xml: <property name="<Alt>F1" type="string" value="xfce4-popup-whiskermenu --pointer"/>
There is another post from 6 years ago about this problem's past incarnation here but neither that question nor the answers are of use to this problem sadly.