Basta adicionar o ponto no conjunto de "caracteres permitidos". Adicione também o caractere /
(parte do caminho).
for f in ./*; do
new_f="$( printf "%s" "$f" | tr ' []' '-' | tr -dc 'A-Za-z0-9_./-' | tr '[:upper:]' '[:lower:]')"
printf "Would move '%s' to '%s'\n" "$f" "$new_f"
done
Isso resulta em
Would move './St Nicholas' church from NE [1235] 1936-08-01.jpg' to './st-nicholas-church-from-ne--1235--1936-08-01.jpg'