All of the VA xxx items in the Text Editor section are for the foreground and background highlighting that VA applies inside the text editor, and also inside its various windows, if you have told VA to apply its syntax colouring outside of the editor.
For Find References, consider this very simple code sample:
// run VA Find References on "nLocalVar"
// on the next two lines it is coloured with "VA Find Reference (Modified)"
int nLocalVar = 2, nTarget;
nLocalVar += 2;
// on this line it is coloured with "VA Find Reference"
nTarget = nLocalVar;
assuming in the Find References Results window you have turned On "Highlight all" and in the VA options dialog you have turned on syntax highlighting for views, then the VA Find References colours will be applied to both the editor and the Find References Results window, to both highlight the references in the code, and to also show you if the reference is being modified or just used without modifying it.
Does this make sense?