Ok, after playing around with this, thankfully, I have come to a solution.
I'll share it and hope this might help others with the same problem.
Editing my ~/.config/menus/xfce-applications.menu does nothing, so, I edited /etc/xdg/menus/xfce-applications.menu as root and focused on the <Layout> section.
After realizing that some of the .desktop files under /usr/share/applications are named differently (e.g. former xfce4-logout.desktop is now called xfce4-session-logout.desktop), I started adding the correct names into <Layout> section and they magically moved from the menu to the top section of the menu, and voila; I achieved what I wanted.
This is my final <Layout> section:
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