Reading the docs it appears if you right click a feature in the vertex editor it will lock to that feature (Note this is introduced at QGIS 3.4):
Right click on a feature will immediately show the vertex editor and lock this feature, thus disabling the editing of any other features. While being locked, a feature is exclusive for editing: Selecting and moving of vertices and segments by clicking or dragging is only possible for this feature. New vertices can only be added to the locked feature.
Alternatively, you could select a vertex next to or near the one you want and cycle through the table to grab the correct one.
I.e. Select a vertex from the correct feature where it is not overlapping (so you can easily select it), then cycle up/down through the table in the Panel until it highlights the one you wanted to delete.
See docs below for more info on the Panel.
https://docs.qgis.org/3.16/en/docs/user_manual/working_with_vector/editing_geometry_attributes.html#the-vertex-editor-panel