I tried:
let g:better_whitespace_enabled=1
let g:strip_whitelines_at_eof=1
let g:strip_whitespace_on_save=1
and
let g:better_whitespace_enabled=1
let g:better_whitespace_filetypes_blacklist=['diff', 'gitcommit', 'unite', 'qf', 'help', 'markdown']
let g:strip_whitelines_at_eof=1
let g:strip_whitespace_on_save=1
and with both configurations I had the confirmation prompt in markdown files.
Is there something I'm doing wrong?