for me and its only my opinion
if i lost the fender i would learn to ride with a back pack
if you tour or need the storage i would ad a top box and leave the fender
on this bike i ride with a backpack and i have fenders
but most of my bikes have top boxes and i use shad
to answer your question though if you bury the rear light under all that rack and box you may lose the visibility to the people behind you
and the people behind you are already trying to kill you, and they need as little help as possible
for me i like a very visible rear light