The issue is caused by the sensible plugin:line 93. :help t_Co
" Allow color schemes to do bright colors without forcing bold.
if &t_Co == 8 && $TERM !~# '^linux'
  set t_Co=16  " << --- Causes hickup
endif
 If you run vim in verbose log mode (vim -V15load_log.vim) – and search
for t_Co= and RedundantSpaces you'll see that sensible is actually parsed after your appearance.vim file.
 Quick fix would be to either comment out that section of the code and add it to your .vimrc, but as you link to git repositories that is perhaps not what you want.
 A different approach would be to move it out of the bundledirectory and add it as a separate source line in your vimrc, before your glob loop.
I.e.:
  source ~/.vim/hacks/vim-sensible/plugin/sensible.vim
  for f in split(glob ...
Another way would be to load custom highlight on BufLoad.
Etc. …