In the second invocation, you have an extra "t" after "C:\ ... \python.exe".
I think your command should be (assuming the input.csv and multiple_index_words.py are also in "D:\Penelope\penelope-3.1.3"):
Code:
C:\Users\Oren\AppData\Local\Programs\Python\Python35-32\python.exe -m penelope -i input.csv -j csv --csv-fs "\\t" -f en -t en -p xml -o output_with_input_parser.xml --input-parser multiple_index_words.py
(I am not sure "\\t" is the right escape for windows. Maybe it is just "\t". Use what works for you.)